SKIP_DOCS_VALIDATIONtrueSKIP_DOCS_VALIDATIONBooleanParameterDefinitionhttps://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/BIOFORMATS-buildBIOFORMATS-buildBIOFORMATS-buildBIOFORMATS-buildhttps://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/trueStarted by upstream project "Trigger" build number 118118Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue100440badce7006c269044aed9d9e223062cf8940e0440badce7006c269044aed9d9e223062cf8940e0origin/merge_ci440badce7006c269044aed9d9e223062cf8940e0440badce7006c269044aed9d9e223062cf8940e0origin/merge_ci440badce7006c269044aed9d9e223062cf8940e0440badce7006c269044aed9d9e223062cf8940e0origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#100601062626729BIOFORMATS-build #100100falsefalse1003683SUCCESS1791065284122https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/100/testintegration0f56ae9e3c5d57fb5ddbe7cb8cdffaca70e83a681791064887000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#146 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/146/) 2026-10-03 22:01:27 +00000f56ae9e3c5d57fb5ddbe7cb8cdffaca70e83a68merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit440badce7006c269044aed9d9e223062cf8940e01791065216000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..cf21ea57 Previously merged: - PR 487 pwalczysko 'Gatan2' - PR 486 pwalczysko 'Exclude gatan urls: 429 too many redirects' - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..9d5baf57d7 Previously merged: - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4487 sbesson 'TiffParser: log failed endian check at DEBUG level' - PR 4486 melissalinkert 'Upgrade check cleanup' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#146 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/146/) 2026-10-03 22:06:56 +0000440badce7006c269044aed9d9e223062cf8940e0merge master -Dorg -Ssuccess-onlyeditome-jaieditome-mdbtoolseditome-metakiteditbio-formats-documentationeditome-common-javaeditome-modeleditZarrReadereditome-codecseditome-stubsedit.gitmoduleseditome-poieditbio-formats-exampleseditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop100https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/100/Started by upstream project "Trigger" build number 117117Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue998239bbeed1b99efb18983a2b43a91369826ab6958239bbeed1b99efb18983a2b43a91369826ab695origin/merge_ci8239bbeed1b99efb18983a2b43a91369826ab6958239bbeed1b99efb18983a2b43a91369826ab695origin/merge_ci8239bbeed1b99efb18983a2b43a91369826ab6958239bbeed1b99efb18983a2b43a91369826ab695origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#99620915626729BIOFORMATS-build #9999falsefalse993637SUCCESS1790978901160https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/99/testintegration422bc4d3e966d30b4c4c5cda1a40e8c364b6494a1790978491000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#145 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/145/) 2026-10-02 22:01:31 +0000422bc4d3e966d30b4c4c5cda1a40e8c364b6494amerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit8239bbeed1b99efb18983a2b43a91369826ab6951790978830000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..cf21ea57 Previously merged: - PR 487 pwalczysko 'Gatan2' - PR 486 pwalczysko 'Exclude gatan urls: 429 too many redirects' - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..9d5baf57d7 Previously merged: - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4487 sbesson 'TiffParser: log failed endian check at DEBUG level' - PR 4486 melissalinkert 'Upgrade check cleanup' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#145 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/145/) 2026-10-02 22:07:10 +00008239bbeed1b99efb18983a2b43a91369826ab695merge master -Dorg -Ssuccess-onlyeditome-common-javaeditome-poieditbioformatseditome-codecseditome-mdbtoolsedit.gitmoduleseditbio-formats-exampleseditome-metakiteditZarrReadereditome-jaieditome-modeleditbio-formats-documentationeditome-stubsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop99https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/99/Started by upstream project "Trigger" build number 116116Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue9822adab0a5d27bf6f8f6f4dde11a98c8e15a20e0e22adab0a5d27bf6f8f6f4dde11a98c8e15a20e0eorigin/merge_ci22adab0a5d27bf6f8f6f4dde11a98c8e15a20e0e22adab0a5d27bf6f8f6f4dde11a98c8e15a20e0eorigin/merge_ci22adab0a5d27bf6f8f6f4dde11a98c8e15a20e0e22adab0a5d27bf6f8f6f4dde11a98c8e15a20e0eorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#98658211626729BIOFORMATS-build #9898falsefalse983586SUCCESS1790892513562https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/98/testintegration588559848ed719ebaffb3ba006998ee0077968241790892089000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#144 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/144/) 2026-10-01 22:01:29 +0000588559848ed719ebaffb3ba006998ee007796824merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit22adab0a5d27bf6f8f6f4dde11a98c8e15a20e0e1790892444000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..cf21ea57 Previously merged: - PR 487 pwalczysko 'Gatan2' - PR 486 pwalczysko 'Exclude gatan urls: 429 too many redirects' - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d01c1aa090 Previously merged: - PR 4487 sbesson 'TiffParser: log failed endian check at DEBUG level' - PR 4486 melissalinkert 'Upgrade check cleanup' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#144 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/144/) 2026-10-01 22:07:24 +000022adab0a5d27bf6f8f6f4dde11a98c8e15a20e0emerge master -Dorg -Ssuccess-onlyeditome-mdbtoolseditbio-formats-exampleseditome-stubseditbio-formats-documentationedit.gitmoduleseditome-jaieditbioformatseditome-common-javaeditome-poieditome-codecseditome-metakiteditome-modeleditZarrReadergithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop98https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/98/Started by upstream project "Trigger" build number 115115Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue97a05dc995bd836181e65f03a7814d167bf8f64624a05dc995bd836181e65f03a7814d167bf8f64624origin/merge_cia05dc995bd836181e65f03a7814d167bf8f64624a05dc995bd836181e65f03a7814d167bf8f64624origin/merge_cia05dc995bd836181e65f03a7814d167bf8f64624a05dc995bd836181e65f03a7814d167bf8f64624origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#97625975626729BIOFORMATS-build #9797falsefalse973530SUCCESS1790806105568https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/97/testintegrationd4ebf8d2555dcd5afc399ae3fbcb0587daae10191790805688000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#143 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/143/) 2026-09-30 22:01:28 +0000d4ebf8d2555dcd5afc399ae3fbcb0587daae1019merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakita05dc995bd836181e65f03a7814d167bf8f646241790806038000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..cf21ea57 Previously merged: - PR 487 pwalczysko 'Gatan2' - PR 486 pwalczysko 'Exclude gatan urls: 429 too many redirects' - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d01c1aa090 Previously merged: - PR 4487 sbesson 'TiffParser: log failed endian check at DEBUG level' - PR 4486 melissalinkert 'Upgrade check cleanup' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#143 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/143/) 2026-09-30 22:07:18 +0000a05dc995bd836181e65f03a7814d167bf8f64624merge master -Dorg -Ssuccess-onlyeditome-stubseditome-poieditZarrReadereditome-mdbtoolseditbioformatsedit.gitmoduleseditome-jaieditbio-formats-exampleseditome-modeleditome-codecseditome-common-javaeditome-metakiteditbio-formats-documentationgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop97https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/97/Started by upstream project "Trigger" build number 114114Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue96bf48e68f5b7e9910647961af70917a091ad9aa38bf48e68f5b7e9910647961af70917a091ad9aa38origin/merge_cibf48e68f5b7e9910647961af70917a091ad9aa38bf48e68f5b7e9910647961af70917a091ad9aa38origin/merge_cibf48e68f5b7e9910647961af70917a091ad9aa38bf48e68f5b7e9910647961af70917a091ad9aa38origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#96638516626729BIOFORMATS-build #9696falsefalse963472SUCCESS1790719737520https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/96/testintegration1834c36941338dbe2f5ad2cdf969a28e7146aca51790719328000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#142 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/142/) 2026-09-29 22:02:08 +00001834c36941338dbe2f5ad2cdf969a28e7146aca5merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitbf48e68f5b7e9910647961af70917a091ad9aa381790719670000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..feda4958 Previously merged: - PR 486 pwalczysko 'Exclude gatan urls: 429 too many redirects' - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' - PR 487 pwalczysko 'Gatan2' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d01c1aa090 Previously merged: - PR 4487 sbesson 'TiffParser: log failed endian check at DEBUG level' - PR 4486 melissalinkert 'Upgrade check cleanup' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#142 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/142/) 2026-09-29 22:07:50 +0000bf48e68f5b7e9910647961af70917a091ad9aa38merge master -Dorg -Ssuccess-onlyeditome-modeleditome-stubseditZarrReadereditome-common-javaeditome-jaieditome-poieditbioformatseditome-codecsedit.gitmoduleseditbio-formats-exampleseditome-metakiteditome-mdbtoolseditbio-formats-documentationgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop96https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/96/Started by upstream project "Trigger" build number 113113Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue9542442fab402780e4368156279453161468441fe442442fab402780e4368156279453161468441fe4origin/merge_ci42442fab402780e4368156279453161468441fe442442fab402780e4368156279453161468441fe4origin/merge_ci42442fab402780e4368156279453161468441fe442442fab402780e4368156279453161468441fe4origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#95592925626729BIOFORMATS-build #9595falsefalse953427SUCCESS1790633305812https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/95/testintegration3a526232f97800e51a1b872007437aa12cd4f38c1790632881000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#141 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/141/) 2026-09-28 22:01:21 +00003a526232f97800e51a1b872007437aa12cd4f38cmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit42442fab402780e4368156279453161468441fe41790633238000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..feda4958 Previously merged: - PR 486 pwalczysko 'Exclude gatan urls: 429 too many redirects' - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d01c1aa090 Previously merged: - PR 4487 sbesson 'TiffParser: log failed endian check at DEBUG level' - PR 4486 melissalinkert 'Upgrade check cleanup' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#141 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/141/) 2026-09-28 22:07:18 +000042442fab402780e4368156279453161468441fe4merge master -Dorg -Ssuccess-onlyeditome-stubseditbioformatseditome-modeleditome-codecseditZarrReadereditbio-formats-documentationeditome-mdbtoolseditome-poieditbio-formats-exampleseditome-metakiteditome-jaiedit.gitmoduleseditome-common-javagithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop95https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/95/Started by upstream project "Trigger" build number 112112Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue94a27a2ebf9f5cf2f10d74760b3b625e2c56128d4da27a2ebf9f5cf2f10d74760b3b625e2c56128d4dorigin/merge_cia27a2ebf9f5cf2f10d74760b3b625e2c56128d4da27a2ebf9f5cf2f10d74760b3b625e2c56128d4dorigin/merge_cia27a2ebf9f5cf2f10d74760b3b625e2c56128d4da27a2ebf9f5cf2f10d74760b3b625e2c56128d4dorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#94907245626729BIOFORMATS-build #9494falsefalse943380SUCCESS1790546918096https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/94/testintegrationc558efa0e490a59ea7b2dcb605a62bb1538c04531790546487000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#140 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/140/) 2026-09-27 22:01:27 +0000c558efa0e490a59ea7b2dcb605a62bb1538c0453merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakita27a2ebf9f5cf2f10d74760b3b625e2c56128d4d1790546844000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..fc61073a Previously merged: - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..f4277f016d Previously merged: - PR 4486 melissalinkert 'Upgrade check cleanup' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#140 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/140/) 2026-09-27 22:07:24 +0000a27a2ebf9f5cf2f10d74760b3b625e2c56128d4dmerge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditome-codecseditome-metakiteditome-stubseditbioformatsedit.gitmoduleseditome-modeleditome-common-javaeditZarrReadereditbio-formats-exampleseditome-mdbtoolseditome-poieditome-jaigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop94https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/94/Started by upstream project "Trigger" build number 111111Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue93e9b05bdc3bc24b8b0cc0d94a494b4c21e90ca9bde9b05bdc3bc24b8b0cc0d94a494b4c21e90ca9bdorigin/merge_cie9b05bdc3bc24b8b0cc0d94a494b4c21e90ca9bde9b05bdc3bc24b8b0cc0d94a494b4c21e90ca9bdorigin/merge_cie9b05bdc3bc24b8b0cc0d94a494b4c21e90ca9bde9b05bdc3bc24b8b0cc0d94a494b4c21e90ca9bdorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#93588886626729BIOFORMATS-build #9393falsefalse933336SUCCESS1790460465524https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/93/testintegratione5d2c56bbd85b2b6f308d9c956871c2bdc4ddd661790460074000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#139 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/139/) 2026-09-26 22:01:14 +0000e5d2c56bbd85b2b6f308d9c956871c2bdc4ddd66merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakite9b05bdc3bc24b8b0cc0d94a494b4c21e90ca9bd1790460398000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..fc61073a Previously merged: - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..f4277f016d Previously merged: - PR 4486 melissalinkert 'Upgrade check cleanup' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#139 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/139/) 2026-09-26 22:06:38 +0000e9b05bdc3bc24b8b0cc0d94a494b4c21e90ca9bdmerge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditome-mdbtoolseditome-common-javaeditome-poieditbio-formats-documentationeditbioformatseditome-modeleditome-stubsedit.gitmoduleseditome-codecseditome-metakiteditZarrReadereditome-jaigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop93https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/93/Started by upstream project "Trigger" build number 110110Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue9297954db67b5bb6aa658c00ae791a4fba5f4f6ffe97954db67b5bb6aa658c00ae791a4fba5f4f6ffeorigin/merge_ci97954db67b5bb6aa658c00ae791a4fba5f4f6ffe97954db67b5bb6aa658c00ae791a4fba5f4f6ffeorigin/merge_ci97954db67b5bb6aa658c00ae791a4fba5f4f6ffe97954db67b5bb6aa658c00ae791a4fba5f4f6ffeorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#92567671626729BIOFORMATS-build #9292falsefalse923292SUCCESS1790374077161https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/92/testintegration0ccbdc8778270fa543266a079d0e35bcd3cf668e1790373673000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#138 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/138/) 2026-09-25 22:01:13 +00000ccbdc8778270fa543266a079d0e35bcd3cf668emerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit97954db67b5bb6aa658c00ae791a4fba5f4f6ffe1790374008000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..fc61073a Previously merged: - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..f4277f016d Previously merged: - PR 4486 melissalinkert 'Upgrade check cleanup' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#138 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/138/) 2026-09-25 22:06:48 +000097954db67b5bb6aa658c00ae791a4fba5f4f6ffemerge master -Dorg -Ssuccess-onlyeditome-codecseditome-poieditome-common-javaeditome-modeleditbio-formats-exampleseditome-mdbtoolseditZarrReadereditbio-formats-documentationeditome-metakitedit.gitmoduleseditbioformatseditome-jaieditome-stubsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop92https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/92/Started by upstream project "Trigger" build number 109109Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue916953f1bbea1e9f452144e0be7e7fd38ae37490516953f1bbea1e9f452144e0be7e7fd38ae3749051origin/merge_ci6953f1bbea1e9f452144e0be7e7fd38ae37490516953f1bbea1e9f452144e0be7e7fd38ae3749051origin/merge_ci6953f1bbea1e9f452144e0be7e7fd38ae37490516953f1bbea1e9f452144e0be7e7fd38ae3749051origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#91581803626729BIOFORMATS-build #9191falsefalse913246SUCCESS1790337115973https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/91/testintegration9555adc98405482edc869affb1a8d525fa5501be1790336718000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#137 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/137/) 2026-09-25 11:45:18 +00009555adc98405482edc869affb1a8d525fa5501bemerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit6953f1bbea1e9f452144e0be7e7fd38ae37490511790337048000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..fc61073a Previously merged: - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..f4277f016d Previously merged: - PR 4486 melissalinkert 'Upgrade check cleanup' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#137 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/137/) 2026-09-25 11:50:48 +00006953f1bbea1e9f452144e0be7e7fd38ae3749051merge master -Dorg -Ssuccess-onlyeditome-jaieditbioformatseditome-common-javaeditome-mdbtoolseditome-metakiteditome-codecseditome-poiedit.gitmoduleseditome-modeleditZarrReadereditome-stubseditbio-formats-exampleseditbio-formats-documentationgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop91https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/91/Started by upstream project "Trigger" build number 108108Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue903d7429270714680611490771277b358620a63e2f3d7429270714680611490771277b358620a63e2forigin/merge_ci3d7429270714680611490771277b358620a63e2f3d7429270714680611490771277b358620a63e2forigin/merge_ci3d7429270714680611490771277b358620a63e2f3d7429270714680611490771277b358620a63e2forigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#90606762626729BIOFORMATS-build #9090falsefalse903204SUCCESS1790287684115https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/90/testintegration1cb6cb0571986bc7f3071d2431d4c83f5ffab4871790287276000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#136 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/136/) 2026-09-24 22:01:16 +00001cb6cb0571986bc7f3071d2431d4c83f5ffab487merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit3d7429270714680611490771277b358620a63e2f1790287616000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..fc61073a Previously merged: - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..f4277f016d Previously merged: - PR 4486 melissalinkert 'Upgrade check cleanup' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#136 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/136/) 2026-09-24 22:06:56 +00003d7429270714680611490771277b358620a63e2fmerge master -Dorg -Ssuccess-onlyeditome-metakiteditome-jaieditome-codecseditbio-formats-exampleseditbioformatseditbio-formats-documentationeditome-poieditZarrReadereditome-modeleditome-mdbtoolseditome-common-javaeditome-stubsedit.gitmodulesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop90https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/90/Started by upstream project "Trigger" build number 107107Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue89808872a13b41652ccbc2c6c5392702d4163b5346808872a13b41652ccbc2c6c5392702d4163b5346origin/merge_ci808872a13b41652ccbc2c6c5392702d4163b5346808872a13b41652ccbc2c6c5392702d4163b5346origin/merge_ci808872a13b41652ccbc2c6c5392702d4163b5346808872a13b41652ccbc2c6c5392702d4163b5346origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#89527742626729BIOFORMATS-build #8989falsefalse893157SUCCESS1790201271010https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/89/testintegrationDockerfilecf60ff8657e65932a147a7dccdbd820bd3ba12681790185705000https://merge-ci.openmicroscopy.org/jenkins/user/p.walczyskop.walczyskop.walczysko@dundee.ac.ukUse Debian Bullseye snapshot for Docker build 2026-09-23 18:48:25 +0100cf60ff8657e65932a147a7dccdbd820bd3ba1268Use Debian Bullseye snapshot for Docker buildeditDockerfileDockerfile198f320e9d8deb826fe907dbd333b20b955c5da51790186966000https://merge-ci.openmicroscopy.org/jenkins/user/p.walczyskop.walczyskop.walczysko@dundee.ac.ukOnly use the [check-valid-until=no] specifically for the snapshots 2026-09-23 19:09:26 +0100198f320e9d8deb826fe907dbd333b20b955c5da5Only use the [check-valid-until=no] specifically for the snapshotseditDockerfileDockerfile78d4742138be07d1e5481fdad0a02b171328578e1790187949000https://merge-ci.openmicroscopy.org/jenkins/user/p.walczyskop.walczyskop.walczysko@dundee.ac.ukFix duplicate USER root 2026-09-23 19:25:49 +010078d4742138be07d1e5481fdad0a02b171328578eFix duplicate USER rooteditDockerfiledc7683b4a3b1d7f222ec810d9c3603470be8ea6e1790200867000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Merged PRs: - PR 732 pwalczysko 'Use Debian Bullseye snapshot for Docker build' Generated by BIOFORMATS-push#135 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/135/) 2026-09-23 22:01:07 +0000dc7683b4a3b1d7f222ec810d9c3603470be8ea6emerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit808872a13b41652ccbc2c6c5392702d4163b53461790201205000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Merged PRs: - PR 732 pwalczysko 'Use Debian Bullseye snapshot for Docker build' Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..fc61073a Previously merged: - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..f4277f016d Previously merged: - PR 4486 melissalinkert 'Upgrade check cleanup' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#135 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/135/) 2026-09-23 22:06:45 +0000808872a13b41652ccbc2c6c5392702d4163b5346merge master -Dorg -Ssuccess-onlyeditome-modeleditome-jaieditome-mdbtoolseditome-common-javaeditome-stubseditZarrReadereditbio-formats-exampleseditbio-formats-documentationeditome-codecseditbioformatsedit.gitmoduleseditome-metakiteditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecophttps://merge-ci.openmicroscopy.org/jenkins/user/p.walczyskop.walczysko89https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/89/Started by upstream project "Trigger" build number 106106Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue88fe5406c74deb09bbdd7086ef61fa47130937246ffe5406c74deb09bbdd7086ef61fa47130937246forigin/merge_cife5406c74deb09bbdd7086ef61fa47130937246ffe5406c74deb09bbdd7086ef61fa47130937246forigin/merge_cife5406c74deb09bbdd7086ef61fa47130937246ffe5406c74deb09bbdd7086ef61fa47130937246forigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#88511363626729BIOFORMATS-build #8888falsefalse883144SUCCESS1790150998965https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/88/testintegration31da1bf8961272ba66fa57376c64e061d76a52f41790150603000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#134 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/134/) 2026-09-23 08:03:23 +000031da1bf8961272ba66fa57376c64e061d76a52f4merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitfe5406c74deb09bbdd7086ef61fa47130937246f1790150939000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..fc61073a Previously merged: - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..f4277f016d Previously merged: - PR 4486 melissalinkert 'Upgrade check cleanup' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#134 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/134/) 2026-09-23 08:08:59 +0000fe5406c74deb09bbdd7086ef61fa47130937246fmerge master -Dorg -Ssuccess-onlyeditZarrReadereditome-mdbtoolseditbio-formats-exampleseditome-common-javaeditome-stubseditome-poiedit.gitmoduleseditbio-formats-documentationeditbioformatseditome-jaieditome-modeleditome-metakiteditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop88https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/88/Started by upstream project "Trigger" build number 105105Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue874478c0a2a385d140840f215c27104002a2dd9c9f4478c0a2a385d140840f215c27104002a2dd9c9forigin/merge_ci4478c0a2a385d140840f215c27104002a2dd9c9f4478c0a2a385d140840f215c27104002a2dd9c9forigin/merge_ci4478c0a2a385d140840f215c27104002a2dd9c9f4478c0a2a385d140840f215c27104002a2dd9c9forigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#87634456626729BIOFORMATS-build #8787falsefalse873138SUCCESS1790114862687https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/87/testintegrationfdceac3aa1f9c67ce463db1f26ffbc170fffa4eb1790114468000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#133 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/133/) 2026-09-22 22:01:08 +0000fdceac3aa1f9c67ce463db1f26ffbc170fffa4ebmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit4478c0a2a385d140840f215c27104002a2dd9c9f1790114800000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..fc61073a Previously merged: - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..f4277f016d Previously merged: - PR 4486 melissalinkert 'Upgrade check cleanup' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#133 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/133/) 2026-09-22 22:06:40 +00004478c0a2a385d140840f215c27104002a2dd9c9fmerge master -Dorg -Ssuccess-onlyedit.gitmoduleseditbio-formats-documentationeditome-mdbtoolseditbio-formats-exampleseditome-metakiteditome-jaieditbioformatseditome-codecseditome-modeleditZarrReadereditome-common-javaeditome-poieditome-stubsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop87https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/87/Started by upstream project "Trigger" build number 104104Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue8666259c5ce1c6c8293173d05d21be38df6da7d7e666259c5ce1c6c8293173d05d21be38df6da7d7e6origin/merge_ci66259c5ce1c6c8293173d05d21be38df6da7d7e666259c5ce1c6c8293173d05d21be38df6da7d7e6origin/merge_ci66259c5ce1c6c8293173d05d21be38df6da7d7e666259c5ce1c6c8293173d05d21be38df6da7d7e6origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#86580337626729BIOFORMATS-build #8686falsefalse863076SUCCESS1790028484551https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/86/testintegration813809b491100a75222f99659e60904a2dfa4fd01790028076000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#131 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/131/) 2026-09-21 22:01:16 +0000813809b491100a75222f99659e60904a2dfa4fd0merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit66259c5ce1c6c8293173d05d21be38df6da7d7e61790028418000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..fc61073a Previously merged: - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..8a882a5437 Previously merged: - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4485 melissalinkert 'Operetta: normalize file separators' - PR 4486 melissalinkert 'Upgrade check cleanup' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#131 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/131/) 2026-09-21 22:06:58 +000066259c5ce1c6c8293173d05d21be38df6da7d7e6merge master -Dorg -Ssuccess-onlyeditome-common-javaeditome-mdbtoolseditome-poieditome-stubseditome-modeledit.gitmoduleseditbio-formats-exampleseditome-jaieditbioformatseditbio-formats-documentationeditome-metakiteditZarrReadereditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop86https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/86/Started by upstream project "Trigger" build number 103103Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue85bc9ad8b2b92fb0c7c7fc09eebad1bde449354e7cbc9ad8b2b92fb0c7c7fc09eebad1bde449354e7corigin/merge_cibc9ad8b2b92fb0c7c7fc09eebad1bde449354e7cbc9ad8b2b92fb0c7c7fc09eebad1bde449354e7corigin/merge_cibc9ad8b2b92fb0c7c7fc09eebad1bde449354e7cbc9ad8b2b92fb0c7c7fc09eebad1bde449354e7corigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#85552835626729BIOFORMATS-build #8585falsefalse853028SUCCESS1789942075802https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/85/testintegrationc32555f891ce89ffffe2bd14e59e2c6d953cb6e41789941674000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#130 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/130/) 2026-09-20 22:01:14 +0000c32555f891ce89ffffe2bd14e59e2c6d953cb6e4merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitbc9ad8b2b92fb0c7c7fc09eebad1bde449354e7c1789942008000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..fc61073a Previously merged: - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..8a882a5437 Previously merged: - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4485 melissalinkert 'Operetta: normalize file separators' - PR 4486 melissalinkert 'Upgrade check cleanup' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#130 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/130/) 2026-09-20 22:06:48 +0000bc9ad8b2b92fb0c7c7fc09eebad1bde449354e7cmerge master -Dorg -Ssuccess-onlyeditome-codecseditome-common-javaeditome-poiedit.gitmoduleseditbio-formats-documentationeditome-stubseditbio-formats-exampleseditbioformatseditZarrReadereditome-metakiteditome-modeleditome-jaieditome-mdbtoolsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop85https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/85/Started by upstream project "Trigger" build number 102102Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue848ed042a60aa4f2f2f27abb676c71ca497b5be2008ed042a60aa4f2f2f27abb676c71ca497b5be200origin/merge_ci8ed042a60aa4f2f2f27abb676c71ca497b5be2008ed042a60aa4f2f2f27abb676c71ca497b5be200origin/merge_ci8ed042a60aa4f2f2f27abb676c71ca497b5be2008ed042a60aa4f2f2f27abb676c71ca497b5be200origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#84556588626729BIOFORMATS-build #8484falsefalse842984SUCCESS1789855670785https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/84/testintegrationcfe009fea38a4f0b6a1ed0b5567b1006c845681b1789855273000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#129 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/129/) 2026-09-19 22:01:13 +0000cfe009fea38a4f0b6a1ed0b5567b1006c845681bmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit8ed042a60aa4f2f2f27abb676c71ca497b5be2001789855605000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..fc61073a Previously merged: - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..8a882a5437 Previously merged: - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4485 melissalinkert 'Operetta: normalize file separators' - PR 4486 melissalinkert 'Upgrade check cleanup' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#129 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/129/) 2026-09-19 22:06:45 +00008ed042a60aa4f2f2f27abb676c71ca497b5be200merge master -Dorg -Ssuccess-onlyeditome-metakiteditome-modeleditbio-formats-documentationeditome-stubseditbio-formats-examplesedit.gitmoduleseditome-mdbtoolseditZarrReadereditome-common-javaeditbioformatseditome-codecseditome-poieditome-jaigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop84https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/84/Started by upstream project "Trigger" build number 101101Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue830c70ceeec28e034b1d77746f0507539bf17b3bc20c70ceeec28e034b1d77746f0507539bf17b3bc2origin/merge_ci0c70ceeec28e034b1d77746f0507539bf17b3bc20c70ceeec28e034b1d77746f0507539bf17b3bc2origin/merge_ci0c70ceeec28e034b1d77746f0507539bf17b3bc20c70ceeec28e034b1d77746f0507539bf17b3bc2origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#83549574626729BIOFORMATS-build #8383falsefalse832940SUCCESS1789769283308https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/83/testintegration677e54702d41ab1541a4c09391851899e09257911789768875000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#128 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/128/) 2026-09-18 22:01:15 +0000677e54702d41ab1541a4c09391851899e0925791merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit0c70ceeec28e034b1d77746f0507539bf17b3bc21789769215000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..fc61073a Previously merged: - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..8a882a5437 Previously merged: - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4485 melissalinkert 'Operetta: normalize file separators' - PR 4486 melissalinkert 'Upgrade check cleanup' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#128 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/128/) 2026-09-18 22:06:55 +00000c70ceeec28e034b1d77746f0507539bf17b3bc2merge master -Dorg -Ssuccess-onlyeditbioformatseditZarrReadereditome-poieditome-metakiteditbio-formats-exampleseditome-jaieditbio-formats-documentationeditome-common-javaeditome-stubseditome-codecsedit.gitmoduleseditome-mdbtoolseditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop83https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/83/Started by upstream project "Trigger" build number 100100Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue82392261ab4292e6a81b365e51e58156d3560549dc392261ab4292e6a81b365e51e58156d3560549dcorigin/merge_ci392261ab4292e6a81b365e51e58156d3560549dc392261ab4292e6a81b365e51e58156d3560549dcorigin/merge_ci392261ab4292e6a81b365e51e58156d3560549dc392261ab4292e6a81b365e51e58156d3560549dcorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#82489012626729BIOFORMATS-build #8282falsefalse822895SUCCESS1789717331830https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/82/testintegrationae9a62759db5570a87e2a0ffce20227e8fba1d531789716923000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#127 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/127/) 2026-09-18 07:35:23 +0000ae9a62759db5570a87e2a0ffce20227e8fba1d53merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit392261ab4292e6a81b365e51e58156d3560549dc1789717267000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..fc61073a Previously merged: - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..c738454b00 Previously merged: - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4485 melissalinkert 'Operetta: normalize file separators' - PR 4486 melissalinkert 'Upgrade check cleanup' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#127 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/127/) 2026-09-18 07:41:07 +0000392261ab4292e6a81b365e51e58156d3560549dcmerge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditbio-formats-documentationeditome-codecseditome-stubseditome-modeleditome-common-javaedit.gitmoduleseditome-jaieditbioformatseditome-mdbtoolseditZarrReadereditome-metakiteditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop82https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/82/Started by upstream project "Trigger" build number 9999Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue81104c6b8661511991da943841049d2d60f02cfd96104c6b8661511991da943841049d2d60f02cfd96origin/merge_ci104c6b8661511991da943841049d2d60f02cfd96104c6b8661511991da943841049d2d60f02cfd96origin/merge_ci104c6b8661511991da943841049d2d60f02cfd96104c6b8661511991da943841049d2d60f02cfd96origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#81577257626729BIOFORMATS-build #8181falsefalse812889SUCCESS1789682890914https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/81/testintegration112097cb815ae02e58a097d2008e08e6b3519a441789682481000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#126 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/126/) 2026-09-17 22:01:21 +0000112097cb815ae02e58a097d2008e08e6b3519a44merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit104c6b8661511991da943841049d2d60f02cfd961789682823000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..fc61073a Previously merged: - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..c738454b00 Previously merged: - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#126 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/126/) 2026-09-17 22:07:03 +0000104c6b8661511991da943841049d2d60f02cfd96merge master -Dorg -Ssuccess-onlyedit.gitmoduleseditbio-formats-exampleseditome-common-javaeditome-jaieditome-poieditZarrReadereditome-modeleditome-stubseditbio-formats-documentationeditome-codecseditome-metakiteditbioformatseditome-mdbtoolsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop81https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/81/Started by upstream project "Trigger" build number 9898Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue80457c018d35b20aa00d8de2e2bbbcc2750402e9f7457c018d35b20aa00d8de2e2bbbcc2750402e9f7origin/merge_ci457c018d35b20aa00d8de2e2bbbcc2750402e9f7457c018d35b20aa00d8de2e2bbbcc2750402e9f7origin/merge_ci457c018d35b20aa00d8de2e2bbbcc2750402e9f7457c018d35b20aa00d8de2e2bbbcc2750402e9f7origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#80590427626729BIOFORMATS-build #8080falsefalse802841SUCCESS1789596473523https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/80/testintegration2b6c32803652a76af4455501cf24a849a1cce30d1789596068000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#125 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/125/) 2026-09-16 22:01:08 +00002b6c32803652a76af4455501cf24a849a1cce30dmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit457c018d35b20aa00d8de2e2bbbcc2750402e9f71789596408000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..fc61073a Previously merged: - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (label: exclude) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..dd9f7f810e Previously merged: - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#125 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/125/) 2026-09-16 22:06:48 +0000457c018d35b20aa00d8de2e2bbbcc2750402e9f7merge master -Dorg -Ssuccess-onlyeditome-codecseditome-modeleditome-metakiteditome-common-javaedit.gitmoduleseditome-mdbtoolseditome-poieditZarrReadereditome-jaieditbio-formats-documentationeditome-stubseditbioformatseditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop80https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/80/Started by upstream project "Trigger" build number 9797Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue79ba205787da52f2db3a1bcf488166e4a0309e4ee1ba205787da52f2db3a1bcf488166e4a0309e4ee1origin/merge_ciba205787da52f2db3a1bcf488166e4a0309e4ee1ba205787da52f2db3a1bcf488166e4a0309e4ee1origin/merge_ciba205787da52f2db3a1bcf488166e4a0309e4ee1ba205787da52f2db3a1bcf488166e4a0309e4ee1origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#79601699626729BIOFORMATS-build #7979falsefalse792797SUCCESS1789510116043https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/79/testintegrationee5dfa9c13e78589884ec89ad09ef2d8eb4befbb1789509720000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#124 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/124/) 2026-09-15 22:02:00 +0000ee5dfa9c13e78589884ec89ad09ef2d8eb4befbbmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitba205787da52f2db3a1bcf488166e4a0309e4ee11789510048000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..39f73d00 Previously merged: - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (label: exclude) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..dd9f7f810e Previously merged: - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#124 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/124/) 2026-09-15 22:07:28 +0000ba205787da52f2db3a1bcf488166e4a0309e4ee1merge master -Dorg -Ssuccess-onlyeditZarrReadereditome-common-javaeditome-jaieditome-metakiteditome-poieditome-codecseditbio-formats-exampleseditome-mdbtoolseditbioformatseditome-modeledit.gitmoduleseditome-stubseditbio-formats-documentationgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop79https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/79/Started by upstream project "Trigger" build number 9696Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue787f3f567c9870866bf47e5c1696358319abaf63f47f3f567c9870866bf47e5c1696358319abaf63f4origin/merge_ci7f3f567c9870866bf47e5c1696358319abaf63f47f3f567c9870866bf47e5c1696358319abaf63f4origin/merge_ci7f3f567c9870866bf47e5c1696358319abaf63f47f3f567c9870866bf47e5c1696358319abaf63f4origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#78609789626729BIOFORMATS-build #7878falsefalse782753SUCCESS1789423708759https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/78/testintegration148b84d286b9b2e2c3626e39a7f97a110dbd83c21789423283000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#123 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/123/) 2026-09-14 22:01:23 +0000148b84d286b9b2e2c3626e39a7f97a110dbd83c2merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit7f3f567c9870866bf47e5c1696358319abaf63f41789423639000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..39f73d00 Previously merged: - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..dd9f7f810e Previously merged: - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' Conflicting PRs (not included): - PR 4479 melissalinkert 'Physical sizes for subresolutions' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#123 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/123/) 2026-09-14 22:07:19 +00007f3f567c9870866bf47e5c1696358319abaf63f4merge master -Dorg -Ssuccess-onlyedit.gitmoduleseditome-mdbtoolseditbioformatseditome-jaieditome-poieditZarrReadereditome-codecseditbio-formats-documentationeditome-metakiteditbio-formats-exampleseditome-modeleditome-common-javaeditome-stubsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop78https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/78/Started by upstream project "Trigger" build number 9595Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue772d344158cb7cd3d84accd71c7fa9748afb40ba162d344158cb7cd3d84accd71c7fa9748afb40ba16origin/merge_ci2d344158cb7cd3d84accd71c7fa9748afb40ba162d344158cb7cd3d84accd71c7fa9748afb40ba16origin/merge_ci2d344158cb7cd3d84accd71c7fa9748afb40ba162d344158cb7cd3d84accd71c7fa9748afb40ba16origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#77647958626729BIOFORMATS-build #7777falsefalse772709SUCCESS1789337281398https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/77/testintegration038c08eb41a573a30918364280cf0fa04020cb651789336883000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#122 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/122/) 2026-09-13 22:01:23 +0000038c08eb41a573a30918364280cf0fa04020cb65merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit2d344158cb7cd3d84accd71c7fa9748afb40ba161789337217000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..39f73d00 Previously merged: - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..dd9f7f810e Previously merged: - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4479 melissalinkert 'Physical sizes for subresolutions' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#122 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/122/) 2026-09-13 22:06:57 +00002d344158cb7cd3d84accd71c7fa9748afb40ba16merge master -Dorg -Ssuccess-onlyeditome-metakiteditZarrReadereditome-poieditome-codecseditbioformatseditome-mdbtoolseditbio-formats-exampleseditome-jaieditome-stubseditbio-formats-documentationedit.gitmoduleseditome-common-javaeditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop77https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/77/Started by upstream project "Trigger" build number 9494Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue768fe065810e5b71d64685b5202fbadf0ed754dca08fe065810e5b71d64685b5202fbadf0ed754dca0origin/merge_ci8fe065810e5b71d64685b5202fbadf0ed754dca08fe065810e5b71d64685b5202fbadf0ed754dca0origin/merge_ci8fe065810e5b71d64685b5202fbadf0ed754dca08fe065810e5b71d64685b5202fbadf0ed754dca0origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#76631852626729BIOFORMATS-build #7676falsefalse762665SUCCESS1789250889002https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/76/testintegration9b2aa74134b2afb5c4a01160fa8af876ef9d693d1789250485000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#121 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/121/) 2026-09-12 22:01:25 +00009b2aa74134b2afb5c4a01160fa8af876ef9d693dmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit8fe065810e5b71d64685b5202fbadf0ed754dca01789250823000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..39f73d00 Previously merged: - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..dd9f7f810e Previously merged: - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4479 melissalinkert 'Physical sizes for subresolutions' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#121 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/121/) 2026-09-12 22:07:03 +00008fe065810e5b71d64685b5202fbadf0ed754dca0merge master -Dorg -Ssuccess-onlyeditZarrReadereditbio-formats-documentationeditbioformatseditome-mdbtoolseditome-poiedit.gitmoduleseditbio-formats-exampleseditome-common-javaeditome-metakiteditome-jaieditome-stubseditome-codecseditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop76https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/76/Started by upstream project "Trigger" build number 9393Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue759ab4f2adff742036a64616398220a34026bc0de49ab4f2adff742036a64616398220a34026bc0de4origin/merge_ci9ab4f2adff742036a64616398220a34026bc0de49ab4f2adff742036a64616398220a34026bc0de4origin/merge_ci9ab4f2adff742036a64616398220a34026bc0de49ab4f2adff742036a64616398220a34026bc0de4origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#75667185626729BIOFORMATS-build #7575falsefalse752621SUCCESS1789164502534https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/75/testintegration2713f03addbaf5f32528e501dddcebf315bb0f101789164092000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#120 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/120/) 2026-09-11 22:01:32 +00002713f03addbaf5f32528e501dddcebf315bb0f10merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit9ab4f2adff742036a64616398220a34026bc0de41789164435000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..39f73d00 Previously merged: - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (status: None) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..dd9f7f810e Previously merged: - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#120 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/120/) 2026-09-11 22:07:15 +00009ab4f2adff742036a64616398220a34026bc0de4merge master -Dorg -Ssuccess-onlyeditome-common-javaedit.gitmoduleseditZarrReadereditome-modeleditbio-formats-exampleseditbio-formats-documentationeditome-mdbtoolseditome-metakiteditome-codecseditome-jaieditome-poieditbioformatseditome-stubsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop75https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/75/Started by upstream project "Trigger" build number 9292Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue74cdd28aa9bef737cbb52e5026cf92bdbbaea3db57cdd28aa9bef737cbb52e5026cf92bdbbaea3db57origin/merge_cicdd28aa9bef737cbb52e5026cf92bdbbaea3db57cdd28aa9bef737cbb52e5026cf92bdbbaea3db57origin/merge_cicdd28aa9bef737cbb52e5026cf92bdbbaea3db57cdd28aa9bef737cbb52e5026cf92bdbbaea3db57origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#74661777626729BIOFORMATS-build #7474falsefalse742613SUCCESS1789078129835https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/74/testintegrationae9f00488f9e7e98f494590e6085f7da2d00a4031789077698000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#119 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/119/) 2026-09-10 22:01:38 +0000ae9f00488f9e7e98f494590e6085f7da2d00a403merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitcdd28aa9bef737cbb52e5026cf92bdbbaea3db571789078063000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..39f73d00 Previously merged: - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..dd9f7f810e Previously merged: - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4479 melissalinkert 'Physical sizes for subresolutions' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#119 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/119/) 2026-09-10 22:07:43 +0000cdd28aa9bef737cbb52e5026cf92bdbbaea3db57merge master -Dorg -Ssuccess-onlyeditome-modeleditome-stubseditbioformatseditbio-formats-documentationeditome-jaieditome-codecsedit.gitmoduleseditome-common-javaeditbio-formats-exampleseditome-mdbtoolseditome-poieditome-metakiteditZarrReadergithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop74https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/74/Started by upstream project "Trigger" build number 9191Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue73c48e9a9bd8241df3f58a5e9cadd1d655e7372981c48e9a9bd8241df3f58a5e9cadd1d655e7372981origin/merge_cic48e9a9bd8241df3f58a5e9cadd1d655e7372981c48e9a9bd8241df3f58a5e9cadd1d655e7372981origin/merge_cic48e9a9bd8241df3f58a5e9cadd1d655e7372981c48e9a9bd8241df3f58a5e9cadd1d655e7372981origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#73705633626729BIOFORMATS-build #7373falsefalse732564SUCCESS1788991737077https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/73/testintegration4caf798ce11b3a8e866c3faa4c3345954ee187391788991329000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#118 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/118/) 2026-09-09 22:02:09 +00004caf798ce11b3a8e866c3faa4c3345954ee18739merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitc48e9a9bd8241df3f58a5e9cadd1d655e73729811788991674000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..dd9f7f810e Previously merged: - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#118 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/118/) 2026-09-09 22:07:54 +0000c48e9a9bd8241df3f58a5e9cadd1d655e7372981merge master -Dorg -Ssuccess-onlyeditome-common-javaeditbioformatseditome-stubseditbio-formats-exampleseditome-codecseditome-modeleditZarrReadereditbio-formats-documentationeditome-jaiedit.gitmoduleseditome-metakiteditome-mdbtoolseditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop73https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/73/Started by upstream project "Trigger" build number 9090Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue72494a6bcf4717dcbdbdbd5a2630c1b24dac6f5654494a6bcf4717dcbdbdbd5a2630c1b24dac6f5654origin/merge_ci494a6bcf4717dcbdbdbd5a2630c1b24dac6f5654494a6bcf4717dcbdbdbd5a2630c1b24dac6f5654origin/merge_ci494a6bcf4717dcbdbdbd5a2630c1b24dac6f5654494a6bcf4717dcbdbdbd5a2630c1b24dac6f5654origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#72557197626729BIOFORMATS-build #7272falsefalse722503SUCCESS1788905274484https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/72/testintegrationc3a80a93eba46e70e7606ca00ace62274a960f181788904872000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#117 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/117/) 2026-09-08 22:01:12 +0000c3a80a93eba46e70e7606ca00ace62274a960f18merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit494a6bcf4717dcbdbdbd5a2630c1b24dac6f56541788905210000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..5b90700612 Previously merged: - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#117 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/117/) 2026-09-08 22:06:50 +0000494a6bcf4717dcbdbdbd5a2630c1b24dac6f5654merge master -Dorg -Ssuccess-onlyeditome-modeleditome-jaieditZarrReadereditome-metakiteditome-stubseditbio-formats-exampleseditbio-formats-documentationeditome-codecsedit.gitmoduleseditome-common-javaeditbioformatseditome-poieditome-mdbtoolsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop72https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/72/Started by upstream project "Trigger" build number 8989Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue71e760933a202996b245f49c9de4aaa4bebb3ab826e760933a202996b245f49c9de4aaa4bebb3ab826origin/merge_cie760933a202996b245f49c9de4aaa4bebb3ab826e760933a202996b245f49c9de4aaa4bebb3ab826origin/merge_cie760933a202996b245f49c9de4aaa4bebb3ab826e760933a202996b245f49c9de4aaa4bebb3ab826origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#71842849626729BIOFORMATS-build #7171falsefalse712453SUCCESS1788869272934https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/71/testintegration4164a01356952f90fc9c2e9d4cc6527061225e7b1788868864000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#116 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/116/) 2026-09-08 12:01:04 +00004164a01356952f90fc9c2e9d4cc6527061225e7bmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakite760933a202996b245f49c9de4aaa4bebb3ab8261788869208000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..5fabd9f7fb Previously merged: - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#116 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/116/) 2026-09-08 12:06:48 +0000e760933a202996b245f49c9de4aaa4bebb3ab826merge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditome-codecseditome-common-javaedit.gitmoduleseditome-metakiteditbioformatseditbio-formats-documentationeditome-jaieditome-poieditZarrReadereditome-stubseditome-modeleditome-mdbtoolsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop71https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/71/Started by upstream project "Trigger" build number 8888Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue700ec322aeedc86a72c36aa6c080cab8f65ccabc0f0ec322aeedc86a72c36aa6c080cab8f65ccabc0forigin/merge_ci0ec322aeedc86a72c36aa6c080cab8f65ccabc0f0ec322aeedc86a72c36aa6c080cab8f65ccabc0forigin/merge_ci0ec322aeedc86a72c36aa6c080cab8f65ccabc0f0ec322aeedc86a72c36aa6c080cab8f65ccabc0forigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#70556327626729BIOFORMATS-build #7070falsefalse702404SUCCESS1788782878358https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/70/testintegration12bf977c66c949be295a21e658a3f76c25c6b22f1788782473000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#113 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/113/) 2026-09-07 12:01:13 +000012bf977c66c949be295a21e658a3f76c25c6b22fmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit0ec322aeedc86a72c36aa6c080cab8f65ccabc0f1788782812000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..5fabd9f7fb Previously merged: - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#113 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/113/) 2026-09-07 12:06:52 +00000ec322aeedc86a72c36aa6c080cab8f65ccabc0fmerge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditome-jaieditbio-formats-documentationeditome-modeleditome-metakiteditome-mdbtoolseditome-codecseditome-stubseditbioformatseditome-common-javaedit.gitmoduleseditZarrReadereditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop70https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/70/Started by upstream project "Trigger" build number 8787Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue699525da933ab81cd05df66772ffeacb86dad6a2639525da933ab81cd05df66772ffeacb86dad6a263origin/merge_ci9525da933ab81cd05df66772ffeacb86dad6a2639525da933ab81cd05df66772ffeacb86dad6a263origin/merge_ci9525da933ab81cd05df66772ffeacb86dad6a2639525da933ab81cd05df66772ffeacb86dad6a263origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#69566271626729BIOFORMATS-build #6969falsefalse692360SUCCESS1788696455817https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/69/testintegratione23ddb6152edea6f3965099491caa8f64c68738d1788696071000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#112 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/112/) 2026-09-06 12:01:11 +0000e23ddb6152edea6f3965099491caa8f64c68738dmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit9525da933ab81cd05df66772ffeacb86dad6a2631788696396000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..5fabd9f7fb Previously merged: - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#112 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/112/) 2026-09-06 12:06:36 +00009525da933ab81cd05df66772ffeacb86dad6a263merge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditome-common-javaedit.gitmoduleseditZarrReadereditome-jaieditome-stubseditome-metakiteditome-mdbtoolseditome-poieditbio-formats-exampleseditome-modeleditome-codecseditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop69https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/69/Started by upstream project "Trigger" build number 8686Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue68d7a48d428b3d470e3928420b68cd42e10a311ed8d7a48d428b3d470e3928420b68cd42e10a311ed8origin/merge_cid7a48d428b3d470e3928420b68cd42e10a311ed8d7a48d428b3d470e3928420b68cd42e10a311ed8origin/merge_cid7a48d428b3d470e3928420b68cd42e10a311ed8d7a48d428b3d470e3928420b68cd42e10a311ed8origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#68671022626729BIOFORMATS-build #6868falsefalse682316SUCCESS1788610058363https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/68/testintegratione5f4687bba7b0bbc417b011ad5592a4d0c989ec61788609676000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#111 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/111/) 2026-09-05 12:01:16 +0000e5f4687bba7b0bbc417b011ad5592a4d0c989ec6merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitd7a48d428b3d470e3928420b68cd42e10a311ed81788609998000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..5fabd9f7fb Previously merged: - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#111 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/111/) 2026-09-05 12:06:38 +0000d7a48d428b3d470e3928420b68cd42e10a311ed8merge master -Dorg -Ssuccess-onlyeditome-codecseditome-common-javaeditome-stubseditome-poieditome-metakitedit.gitmoduleseditbio-formats-exampleseditbioformatseditome-mdbtoolseditome-modeleditome-jaieditZarrReadereditbio-formats-documentationgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop68https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/68/Started by upstream project "Trigger" build number 8181Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue67e3a96af0794adb1a6cc13154b3d09062823e4c0be3a96af0794adb1a6cc13154b3d09062823e4c0borigin/merge_cie3a96af0794adb1a6cc13154b3d09062823e4c0be3a96af0794adb1a6cc13154b3d09062823e4c0borigin/merge_cie3a96af0794adb1a6cc13154b3d09062823e4c0be3a96af0794adb1a6cc13154b3d09062823e4c0borigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#67582063626729BIOFORMATS-build #6767falsefalse672271SUCCESS1788221291718https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/67/testintegration4a09361a24047c4fb014f216e209b374f21df3581788220880000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/98/) 2026-09-01 00:01:20 +00004a09361a24047c4fb014f216e209b374f21df358merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakite3a96af0794adb1a6cc13154b3d09062823e4c0b1788221222000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..5fabd9f7fb Previously merged: - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/98/) 2026-09-01 00:07:02 +0000e3a96af0794adb1a6cc13154b3d09062823e4c0bmerge master -Dorg -Ssuccess-onlyeditome-metakiteditbioformatseditome-codecseditZarrReadereditome-poieditome-common-javaeditome-mdbtoolsedit.gitmoduleseditome-jaieditome-stubseditbio-formats-documentationeditbio-formats-exampleseditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop67https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/67/Started by upstream project "Trigger" build number 8080Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue6681219790a18da4203c6c5b1d6f98877c7c16774081219790a18da4203c6c5b1d6f98877c7c167740origin/merge_ci81219790a18da4203c6c5b1d6f98877c7c16774081219790a18da4203c6c5b1d6f98877c7c167740origin/merge_ci81219790a18da4203c6c5b1d6f98877c7c16774081219790a18da4203c6c5b1d6f98877c7c167740origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#66681498626729BIOFORMATS-build #6666falsefalse662227SUCCESS1788183270606https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/66/testintegration23f9e7311356102888812273a6b9bd1ad8be0d711788182847000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#103 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/103/) 2026-08-31 13:27:27 +000023f9e7311356102888812273a6b9bd1ad8be0d71merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit81219790a18da4203c6c5b1d6f98877c7c1677401788183206000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..b27c5e4fc0 Previously merged: - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#103 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/103/) 2026-08-31 13:33:26 +000081219790a18da4203c6c5b1d6f98877c7c167740merge master -Dorg -Ssuccess-onlyeditome-mdbtoolsedit.gitmoduleseditome-poieditbio-formats-documentationeditome-stubseditbioformatseditbio-formats-exampleseditome-metakiteditome-modeleditome-codecseditome-common-javaeditZarrReadereditome-jaigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop66https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/66/Started by upstream project "Trigger" build number 7878Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue657837d9f6c2d5ec473c5baac03838677eeb1c756b7837d9f6c2d5ec473c5baac03838677eeb1c756borigin/merge_ci7837d9f6c2d5ec473c5baac03838677eeb1c756b7837d9f6c2d5ec473c5baac03838677eeb1c756borigin/merge_ci7837d9f6c2d5ec473c5baac03838677eeb1c756b7837d9f6c2d5ec473c5baac03838677eeb1c756borigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#65628555626729BIOFORMATS-build #6565falsefalse652177SUCCESS1788099908286https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/65/testintegration8272413947309797eeef0df65c6d046977244db71788099549000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#100 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/100/) 2026-08-30 14:19:09 +00008272413947309797eeef0df65c6d046977244db7merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit7837d9f6c2d5ec473c5baac03838677eeb1c756b1788099849000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d0f10ab8fc Previously merged: - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#100 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/100/) 2026-08-30 14:24:09 +00007837d9f6c2d5ec473c5baac03838677eeb1c756bmerge master -Dorg -Ssuccess-onlyeditome-codecseditome-mdbtoolseditbioformatseditbio-formats-exampleseditome-metakiteditome-stubseditome-poiedit.gitmoduleseditbio-formats-documentationeditome-jaieditome-modeleditome-common-javaeditZarrReadergithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop65https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/65/Started by upstream project "Trigger" build number 7676Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue64e9d29aa7c935de797806e6ce9780e9e55fd8464ae9d29aa7c935de797806e6ce9780e9e55fd8464aorigin/merge_cie9d29aa7c935de797806e6ce9780e9e55fd8464ae9d29aa7c935de797806e6ce9780e9e55fd8464aorigin/merge_cie9d29aa7c935de797806e6ce9780e9e55fd8464ae9d29aa7c935de797806e6ce9780e9e55fd8464aorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#64573936626729BIOFORMATS-build #6464falsefalse642129SUCCESS1787996555296https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/64/testintegrationf0990ba393259e8f638f3dcea161662465a781661787996160000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#97 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/97/) 2026-08-29 09:36:00 +0000f0990ba393259e8f638f3dcea161662465a78166merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakite9d29aa7c935de797806e6ce9780e9e55fd8464a1787996492000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d0f10ab8fc Previously merged: - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#97 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/97/) 2026-08-29 09:41:32 +0000e9d29aa7c935de797806e6ce9780e9e55fd8464amerge master -Dorg -Ssuccess-onlyedit.gitmoduleseditome-mdbtoolseditbio-formats-documentationeditome-metakiteditome-stubseditome-common-javaeditome-modeleditome-jaieditZarrReadereditbioformatseditome-poieditbio-formats-exampleseditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop64https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/64/Started by upstream project "Trigger" build number 7373Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue6300ed73314f97ef7ca11664dfb4fc9f947d6130f500ed73314f97ef7ca11664dfb4fc9f947d6130f5origin/merge_ci00ed73314f97ef7ca11664dfb4fc9f947d6130f500ed73314f97ef7ca11664dfb4fc9f947d6130f5origin/merge_ci00ed73314f97ef7ca11664dfb4fc9f947d6130f500ed73314f97ef7ca11664dfb4fc9f947d6130f5origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#63559910626729BIOFORMATS-build #6363falsefalse632043SUCCESS1787875646539https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/63/testintegration7a92d1818478e339b4d926c107cf07ed18afe3531787875285000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#94 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/94/) 2026-08-28 00:01:25 +00007a92d1818478e339b4d926c107cf07ed18afe353merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit00ed73314f97ef7ca11664dfb4fc9f947d6130f51787875591000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' (status: failure) - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' (status: failure) - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d0f10ab8fc Previously merged: - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#94 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/94/) 2026-08-28 00:06:31 +000000ed73314f97ef7ca11664dfb4fc9f947d6130f5merge master -Dorg -Ssuccess-onlyeditome-metakiteditome-stubseditome-modeleditome-mdbtoolseditome-poieditbio-formats-documentationeditome-jaiedit.gitmoduleseditome-codecseditZarrReadereditbioformatseditome-common-javaeditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop63https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/63/Started by upstream project "Trigger" build number 7272Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue62ea201b1f895d6d4670bb53659b80d2f3251d993dea201b1f895d6d4670bb53659b80d2f3251d993dorigin/merge_ciea201b1f895d6d4670bb53659b80d2f3251d993dea201b1f895d6d4670bb53659b80d2f3251d993dorigin/merge_ciea201b1f895d6d4670bb53659b80d2f3251d993dea201b1f895d6d4670bb53659b80d2f3251d993dorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#62522154626729BIOFORMATS-build #6262falsefalse622034SUCCESS1787789284449https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/62/testintegratione76c82fd9ce0cc9e66584a0367fe294cf608d5f61787788875000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#92 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/92/) 2026-08-27 00:01:15 +0000e76c82fd9ce0cc9e66584a0367fe294cf608d5f6merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitea201b1f895d6d4670bb53659b80d2f3251d993d1787789220000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' (status: failure) - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' (status: failure) - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d0f10ab8fc Previously merged: - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#92 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/92/) 2026-08-27 00:07:00 +0000ea201b1f895d6d4670bb53659b80d2f3251d993dmerge master -Dorg -Ssuccess-onlyeditome-jaieditome-codecsedit.gitmoduleseditbioformatseditome-stubseditbio-formats-documentationeditome-common-javaeditbio-formats-exampleseditZarrReadereditome-modeleditome-metakiteditome-poieditome-mdbtoolsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop62https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/62/Started by upstream project "Trigger" build number 7171Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue611102cb7155d63159d76c0c7d4365553f7fa697a11102cb7155d63159d76c0c7d4365553f7fa697a1origin/merge_ci1102cb7155d63159d76c0c7d4365553f7fa697a11102cb7155d63159d76c0c7d4365553f7fa697a1origin/merge_ci1102cb7155d63159d76c0c7d4365553f7fa697a11102cb7155d63159d76c0c7d4365553f7fa697a1origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#61476727626729BIOFORMATS-build #6161falsefalse612025SUCCESS1787733228190https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/61/testintegratione30cbbb45168f85a892ccdb16b197a10f5e287991787732816000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#91 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/91/) 2026-08-26 08:26:56 +0000e30cbbb45168f85a892ccdb16b197a10f5e28799merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit1102cb7155d63159d76c0c7d4365553f7fa697a11787733154000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d0f10ab8fc Previously merged: - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#91 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/91/) 2026-08-26 08:32:34 +00001102cb7155d63159d76c0c7d4365553f7fa697a1merge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditome-metakiteditome-jaieditome-poieditZarrReadereditbio-formats-exampleseditome-mdbtoolsedit.gitmoduleseditome-codecseditome-modeleditome-common-javaeditome-stubseditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop61https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/61/Started by upstream project "Trigger" build number 7070Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue6012156e9dc0200b9ddaba896b554e4e96c9cb625712156e9dc0200b9ddaba896b554e4e96c9cb6257origin/merge_ci12156e9dc0200b9ddaba896b554e4e96c9cb625712156e9dc0200b9ddaba896b554e4e96c9cb6257origin/merge_ci12156e9dc0200b9ddaba896b554e4e96c9cb625712156e9dc0200b9ddaba896b554e4e96c9cb6257origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#60594621626729BIOFORMATS-build #6060falsefalse602019SUCCESS1787702862513https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/60/testintegrationa69b830ba70ab2daf3a01f4e0a3c8d95e12537bd1787702460000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#90 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/90/) 2026-08-26 00:01:00 +0000a69b830ba70ab2daf3a01f4e0a3c8d95e12537bdmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit12156e9dc0200b9ddaba896b554e4e96c9cb62571787702802000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..7a7e175cd5 Previously merged: - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#90 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/90/) 2026-08-26 00:06:42 +000012156e9dc0200b9ddaba896b554e4e96c9cb6257merge master -Dorg -Ssuccess-onlyeditome-stubseditome-poieditbioformatseditome-common-javaeditome-jaiedit.gitmoduleseditbio-formats-documentationeditbio-formats-exampleseditome-metakiteditome-codecseditome-modeleditZarrReadereditome-mdbtoolsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop60https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/60/Started by upstream project "Trigger" build number 6969Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue59f2a16a696756247228e276001ede9fdf59608766f2a16a696756247228e276001ede9fdf59608766origin/merge_cif2a16a696756247228e276001ede9fdf59608766f2a16a696756247228e276001ede9fdf59608766origin/merge_cif2a16a696756247228e276001ede9fdf59608766f2a16a696756247228e276001ede9fdf59608766origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#59596540626729BIOFORMATS-build #5959falsefalse591969SUCCESS1787616581746https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/59/testintegrationb8a30a73cc15ee74dac00b2655c0adcd608c40241787616176000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#88 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/88/) 2026-08-25 00:02:56 +0000b8a30a73cc15ee74dac00b2655c0adcd608c4024merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitf2a16a696756247228e276001ede9fdf596087661787616516000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..7a7e175cd5 Previously merged: - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#88 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/88/) 2026-08-25 00:08:36 +0000f2a16a696756247228e276001ede9fdf59608766merge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditZarrReadereditome-codecseditbio-formats-documentationeditbioformatsedit.gitmoduleseditome-mdbtoolseditome-common-javaeditome-metakiteditome-jaieditome-modeleditome-poieditome-stubsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop59https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/59/Started by upstream project "Trigger" build number 6868Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue580af4cf6d88133c0cb18dbb56e466aacad9442cd60af4cf6d88133c0cb18dbb56e466aacad9442cd6origin/merge_ci0af4cf6d88133c0cb18dbb56e466aacad9442cd60af4cf6d88133c0cb18dbb56e466aacad9442cd6origin/merge_ci0af4cf6d88133c0cb18dbb56e466aacad9442cd60af4cf6d88133c0cb18dbb56e466aacad9442cd6origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#58462173626729BIOFORMATS-build #5858falsefalse581920SUCCESS1787530059716https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/58/testintegration108d434efc9e31ff78fda11b59c66546eeb699de1787529673000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#86 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/86/) 2026-08-24 00:01:13 +0000108d434efc9e31ff78fda11b59c66546eeb699demerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit0af4cf6d88133c0cb18dbb56e466aacad9442cd61787530000000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d87eb853f0 Previously merged: - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (status: action_required) Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#86 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/86/) 2026-08-24 00:06:40 +00000af4cf6d88133c0cb18dbb56e466aacad9442cd6merge master -Dorg -Ssuccess-onlyeditome-metakiteditome-stubseditZarrReadereditome-poieditome-common-javaeditbio-formats-documentationeditome-codecseditome-modeleditbio-formats-exampleseditbioformatseditome-mdbtoolsedit.gitmoduleseditome-jaigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop58https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/58/Started by upstream project "Trigger" build number 6767Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue5723d4d74fc36024e95955c57d9fb0d19f4067773023d4d74fc36024e95955c57d9fb0d19f40677730origin/merge_ci23d4d74fc36024e95955c57d9fb0d19f4067773023d4d74fc36024e95955c57d9fb0d19f40677730origin/merge_ci23d4d74fc36024e95955c57d9fb0d19f4067773023d4d74fc36024e95955c57d9fb0d19f40677730origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#57470151626729BIOFORMATS-build #5757falsefalse571875SUCCESS1787443662809https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/57/testintegrationd4eb863e98e6a6c06851eff9d6ffaefca331bd541787443278000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#84 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/84/) 2026-08-23 00:01:18 +0000d4eb863e98e6a6c06851eff9d6ffaefca331bd54merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit23d4d74fc36024e95955c57d9fb0d19f406777301787443601000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d87eb853f0 Previously merged: - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (status: action_required) Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#84 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/84/) 2026-08-23 00:06:41 +000023d4d74fc36024e95955c57d9fb0d19f40677730merge master -Dorg -Ssuccess-onlyedit.gitmoduleseditome-common-javaeditome-mdbtoolseditome-metakiteditbio-formats-documentationeditome-poieditome-modeleditbio-formats-exampleseditZarrReadereditbioformatseditome-codecseditome-stubseditome-jaigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop57https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/57/Started by upstream project "Trigger" build number 6666Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue56c9627c642071361c145635791a12cbf19a35e126c9627c642071361c145635791a12cbf19a35e126origin/merge_cic9627c642071361c145635791a12cbf19a35e126c9627c642071361c145635791a12cbf19a35e126origin/merge_cic9627c642071361c145635791a12cbf19a35e126c9627c642071361c145635791a12cbf19a35e126origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#56582480626729BIOFORMATS-build #5656falsefalse561831SUCCESS1787357267795https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/56/testintegrationbc074bb2f75f92e5e296c5e5a6d6a7e79b4a1a321787356883000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#83 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/83/) 2026-08-22 00:01:23 +0000bc074bb2f75f92e5e296c5e5a6d6a7e79b4a1a32merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitc9627c642071361c145635791a12cbf19a35e1261787357208000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d87eb853f0 Previously merged: - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (status: failure) Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#83 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/83/) 2026-08-22 00:06:48 +0000c9627c642071361c145635791a12cbf19a35e126merge master -Dorg -Ssuccess-onlyeditome-common-javaeditome-poieditbio-formats-exampleseditome-codecseditZarrReadereditome-stubseditome-jaieditbio-formats-documentationeditome-metakitedit.gitmoduleseditome-mdbtoolseditbioformatseditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop56https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/56/Started by upstream project "Trigger" build number 6565Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue5569c9d37b1069c4c15712c275aa345651537d1c0569c9d37b1069c4c15712c275aa345651537d1c05origin/merge_ci69c9d37b1069c4c15712c275aa345651537d1c0569c9d37b1069c4c15712c275aa345651537d1c05origin/merge_ci69c9d37b1069c4c15712c275aa345651537d1c0569c9d37b1069c4c15712c275aa345651537d1c05origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#55504626626729BIOFORMATS-build #5555falsefalse551767SUCCESS1787270887551https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/55/testintegrationc64e9544cb513914c58f2509bb16921cf7f6d16b1787270495000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#82 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/82/) 2026-08-21 00:01:35 +0000c64e9544cb513914c58f2509bb16921cf7f6d16bmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit69c9d37b1069c4c15712c275aa345651537d1c051787270823000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' (status: None) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d87eb853f0 Previously merged: - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#82 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/82/) 2026-08-21 00:07:03 +000069c9d37b1069c4c15712c275aa345651537d1c05merge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditZarrReadereditome-jaieditome-stubseditbio-formats-exampleseditome-common-javaeditome-modeleditbioformatseditome-codecseditome-metakiteditome-mdbtoolseditome-poiedit.gitmodulesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop55https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/55/Started by upstream project "Trigger" build number 6464Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue54eec0ed7bf3f4d0a366bc62c74ff79b5424b52059eec0ed7bf3f4d0a366bc62c74ff79b5424b52059origin/merge_cieec0ed7bf3f4d0a366bc62c74ff79b5424b52059eec0ed7bf3f4d0a366bc62c74ff79b5424b52059origin/merge_cieec0ed7bf3f4d0a366bc62c74ff79b5424b52059eec0ed7bf3f4d0a366bc62c74ff79b5424b52059origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#54513400626729BIOFORMATS-build #5454falsefalse541754SUCCESS1787225306571https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/54/testintegrationa93b5981f5d6aefef01125433163ca09cd4812361787224918000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#81 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/81/) 2026-08-20 11:21:58 +0000a93b5981f5d6aefef01125433163ca09cd481236merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakiteec0ed7bf3f4d0a366bc62c74ff79b5424b520591787225245000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d87eb853f0 Previously merged: - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#81 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/81/) 2026-08-20 11:27:25 +0000eec0ed7bf3f4d0a366bc62c74ff79b5424b52059merge master -Dorg -Ssuccess-onlyeditome-metakiteditome-modeledit.gitmoduleseditome-poieditome-stubseditbioformatseditome-jaieditZarrReadereditbio-formats-documentationeditome-common-javaeditbio-formats-exampleseditome-codecseditome-mdbtoolsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop54https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/54/Started by upstream project "Trigger" build number 6363Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue536f6d9608dfb76c283c9a8497cc06b98e76f491f16f6d9608dfb76c283c9a8497cc06b98e76f491f1origin/merge_ci6f6d9608dfb76c283c9a8497cc06b98e76f491f16f6d9608dfb76c283c9a8497cc06b98e76f491f1origin/merge_ci6f6d9608dfb76c283c9a8497cc06b98e76f491f16f6d9608dfb76c283c9a8497cc06b98e76f491f1origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#53577607626729BIOFORMATS-build #5353falsefalse531711SUCCESS1787184460599https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/53/testintegration24bdbf1f4658c38f94511cabd90a8d13ba495c8f1787184065000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#80 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/80/) 2026-08-20 00:01:05 +000024bdbf1f4658c38f94511cabd90a8d13ba495c8fmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit6f6d9608dfb76c283c9a8497cc06b98e76f491f11787184398000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d87eb853f0 Previously merged: - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#80 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/80/) 2026-08-20 00:06:38 +00006f6d9608dfb76c283c9a8497cc06b98e76f491f1merge master -Dorg -Ssuccess-onlyedit.gitmoduleseditome-jaieditome-metakiteditbio-formats-documentationeditome-codecseditome-stubseditbio-formats-exampleseditZarrReadereditbioformatseditome-poieditome-common-javaeditome-modeleditome-mdbtoolsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop53https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/53/Started by upstream project "Trigger" build number 6262Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue529aa0367215f5ff405646ecc75567245a8af683ce9aa0367215f5ff405646ecc75567245a8af683ceorigin/merge_ci9aa0367215f5ff405646ecc75567245a8af683ce9aa0367215f5ff405646ecc75567245a8af683ceorigin/merge_ci9aa0367215f5ff405646ecc75567245a8af683ce9aa0367215f5ff405646ecc75567245a8af683ceorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#52651009626729BIOFORMATS-build #5252falsefalse521663SUCCESS1787127791213https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/52/testintegration35d99dac5595bd0b54825a0ca690f8ea259c98801787127413000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#78 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/78/) 2026-08-19 08:16:53 +000035d99dac5595bd0b54825a0ca690f8ea259c9880merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit9aa0367215f5ff405646ecc75567245a8af683ce1787127711000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d87eb853f0 Previously merged: - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#78 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/78/) 2026-08-19 08:21:51 +00009aa0367215f5ff405646ecc75567245a8af683cemerge master -Dorg -Ssuccess-onlyeditome-poieditome-common-javaeditome-mdbtoolseditZarrReadereditome-modeleditome-metakiteditbioformatseditome-stubseditbio-formats-examplesedit.gitmoduleseditbio-formats-documentationeditome-jaieditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop52https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/52/Started by upstream project "Trigger" build number 5959Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue5114f4bd92790cc50852cf28dbeb0ce4893f06d39714f4bd92790cc50852cf28dbeb0ce4893f06d397origin/merge_ci14f4bd92790cc50852cf28dbeb0ce4893f06d39714f4bd92790cc50852cf28dbeb0ce4893f06d397origin/merge_ci14f4bd92790cc50852cf28dbeb0ce4893f06d39714f4bd92790cc50852cf28dbeb0ce4893f06d397origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#51469338626729BIOFORMATS-build #5151falsefalse511612SUCCESS1787011669864https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/51/testintegratione865e86f0636da9e5a906dee933d574c3bdd7fbb1787011280000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#74 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/74/) 2026-08-18 00:01:20 +0000e865e86f0636da9e5a906dee933d574c3bdd7fbbmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit14f4bd92790cc50852cf28dbeb0ce4893f06d3971787011605000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d87eb853f0 Previously merged: - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#74 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/74/) 2026-08-18 00:06:45 +000014f4bd92790cc50852cf28dbeb0ce4893f06d397merge master -Dorg -Ssuccess-onlyeditbioformatseditome-common-javaeditZarrReadereditome-jaieditome-metakiteditome-codecseditome-stubsedit.gitmoduleseditome-mdbtoolseditome-poieditbio-formats-exampleseditbio-formats-documentationeditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop51https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/51/Started by upstream project "Trigger" build number 5858Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue50fb72c65e225d23c6fb34557709af914d689f9995fb72c65e225d23c6fb34557709af914d689f9995origin/merge_cifb72c65e225d23c6fb34557709af914d689f9995fb72c65e225d23c6fb34557709af914d689f9995origin/merge_cifb72c65e225d23c6fb34557709af914d689f9995fb72c65e225d23c6fb34557709af914d689f9995origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#50465467626729BIOFORMATS-build #5050falsefalse501568SUCCESS1786925259886https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/50/testintegrationf2c4c14e51d0371e4471d05c83184e366260df4f1786924883000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#73 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/73/) 2026-08-17 00:01:23 +0000f2c4c14e51d0371e4471d05c83184e366260df4fmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitfb72c65e225d23c6fb34557709af914d689f99951786925201000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d87eb853f0 Previously merged: - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#73 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/73/) 2026-08-17 00:06:41 +0000fb72c65e225d23c6fb34557709af914d689f9995merge master -Dorg -Ssuccess-onlyeditome-metakiteditZarrReadereditome-stubseditome-poieditome-jaieditome-mdbtoolsedit.gitmoduleseditome-common-javaeditbio-formats-documentationeditome-codecseditbio-formats-exampleseditbioformatseditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop50https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/50/Started by upstream project "Trigger" build number 5757Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue493683ea36b09c87dc8cc54d7c8b43e5aa6837c7973683ea36b09c87dc8cc54d7c8b43e5aa6837c797origin/merge_ci3683ea36b09c87dc8cc54d7c8b43e5aa6837c7973683ea36b09c87dc8cc54d7c8b43e5aa6837c797origin/merge_ci3683ea36b09c87dc8cc54d7c8b43e5aa6837c7973683ea36b09c87dc8cc54d7c8b43e5aa6837c797origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#49478700626729BIOFORMATS-build #4949falsefalse491524SUCCESS1786838860016https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/49/testintegration1fb10f193d70a09d1b8e6113eb6b961ad6fbc6951786838474000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#72 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/72/) 2026-08-16 00:01:14 +00001fb10f193d70a09d1b8e6113eb6b961ad6fbc695merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit3683ea36b09c87dc8cc54d7c8b43e5aa6837c7971786838796000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d87eb853f0 Previously merged: - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#72 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/72/) 2026-08-16 00:06:36 +00003683ea36b09c87dc8cc54d7c8b43e5aa6837c797merge master -Dorg -Ssuccess-onlyeditome-common-javaeditbio-formats-exampleseditome-codecseditome-jaieditome-mdbtoolseditome-metakiteditZarrReadereditbio-formats-documentationeditbioformatseditome-poiedit.gitmoduleseditome-stubseditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop49https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/49/Started by upstream project "Trigger" build number 5656Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue484f8f05e05007c7e399d8d3d415ef4798bd39f3194f8f05e05007c7e399d8d3d415ef4798bd39f319origin/merge_ci4f8f05e05007c7e399d8d3d415ef4798bd39f3194f8f05e05007c7e399d8d3d415ef4798bd39f319origin/merge_ci4f8f05e05007c7e399d8d3d415ef4798bd39f3194f8f05e05007c7e399d8d3d415ef4798bd39f319origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#48666398626729BIOFORMATS-build #4848falsefalse481480SUCCESS1786752582226https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/48/testintegrationefc93f31c546d6d095dce345dfa63e4fad3620a21786752153000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#71 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/71/) 2026-08-15 00:02:33 +0000efc93f31c546d6d095dce345dfa63e4fad3620a2merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit4f8f05e05007c7e399d8d3d415ef4798bd39f3191786752511000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..0603cd6b Previously merged: - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d87eb853f0 Previously merged: - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#71 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/71/) 2026-08-15 00:08:31 +00004f8f05e05007c7e399d8d3d415ef4798bd39f319merge master -Dorg -Ssuccess-onlyeditZarrReadereditome-metakiteditbio-formats-documentationeditome-mdbtoolseditome-common-javaedit.gitmoduleseditome-stubseditome-jaieditome-modeleditome-poieditbioformatseditome-codecseditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop48https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/48/Started by upstream project "Trigger" build number 5555Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue47d9e1ba918bc2abb9321e7115cb53ca1bd7c716f2d9e1ba918bc2abb9321e7115cb53ca1bd7c716f2origin/merge_cid9e1ba918bc2abb9321e7115cb53ca1bd7c716f2d9e1ba918bc2abb9321e7115cb53ca1bd7c716f2origin/merge_cid9e1ba918bc2abb9321e7115cb53ca1bd7c716f2d9e1ba918bc2abb9321e7115cb53ca1bd7c716f2origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#47482256626729BIOFORMATS-build #4747falsefalse471436SUCCESS1786666072916https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/47/testintegration29dd83b3596ae138dee95566c0f3415b64aaf1991786665676000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#70 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/70/) 2026-08-14 00:01:16 +000029dd83b3596ae138dee95566c0f3415b64aaf199merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitd9e1ba918bc2abb9321e7115cb53ca1bd7c716f21786666008000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..139b77c1 Previously merged: - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' - PR 483 melissalinkert 'Add section on deprecated API' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4479 melissalinkert 'Physical sizes for subresolutions' (stage: draft) - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..d87eb853f0 Previously merged: - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#70 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/70/) 2026-08-14 00:06:48 +0000d9e1ba918bc2abb9321e7115cb53ca1bd7c716f2merge master -Dorg -Ssuccess-onlyeditome-mdbtoolsedit.gitmoduleseditbio-formats-documentationeditome-codecseditbio-formats-exampleseditome-jaieditome-poieditome-stubseditome-metakiteditbioformatseditome-common-javaeditZarrReadereditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop47https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/47/Started by upstream project "Trigger" build number 5454Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue46f13825ff6ef486f110d2a7684e6445cd47164216f13825ff6ef486f110d2a7684e6445cd47164216origin/merge_cif13825ff6ef486f110d2a7684e6445cd47164216f13825ff6ef486f110d2a7684e6445cd47164216origin/merge_cif13825ff6ef486f110d2a7684e6445cd47164216f13825ff6ef486f110d2a7684e6445cd47164216origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#46491593626729BIOFORMATS-build #4646falsefalse461392SUCCESS1786579665407https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/46/testintegratione0ab8c840ea927001fdf6c5588242726f87b6dd01786579275000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#69 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/69/) 2026-08-13 00:01:15 +0000e0ab8c840ea927001fdf6c5588242726f87b6dd0merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitf13825ff6ef486f110d2a7684e6445cd471642161786579606000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..139b77c1 Previously merged: - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' - PR 483 melissalinkert 'Add section on deprecated API' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..e7f07843b5 Previously merged: - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#69 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/69/) 2026-08-13 00:06:46 +0000f13825ff6ef486f110d2a7684e6445cd47164216merge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditome-poieditome-codecseditome-stubseditZarrReaderedit.gitmoduleseditome-metakiteditome-modeleditbio-formats-documentationeditome-common-javaeditbioformatseditome-jaieditome-mdbtoolsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop46https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/46/Started by upstream project "Trigger" build number 5353Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue453c28fe3f2f16ca89e980180537c427b888ba83203c28fe3f2f16ca89e980180537c427b888ba8320origin/merge_ci3c28fe3f2f16ca89e980180537c427b888ba83203c28fe3f2f16ca89e980180537c427b888ba8320origin/merge_ci3c28fe3f2f16ca89e980180537c427b888ba83203c28fe3f2f16ca89e980180537c427b888ba8320origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#45615309626729BIOFORMATS-build #4545falsefalse451348SUCCESS1786493317389https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/45/testintegration610fe9b6e770568290514f68156c6c31ccb87e961786492928000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#68 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/68/) 2026-08-12 00:02:08 +0000610fe9b6e770568290514f68156c6c31ccb87e96merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit3c28fe3f2f16ca89e980180537c427b888ba83201786493247000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..139b77c1 Previously merged: - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' - PR 483 melissalinkert 'Add section on deprecated API' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..e7f07843b5 Previously merged: - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#68 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/68/) 2026-08-12 00:07:27 +00003c28fe3f2f16ca89e980180537c427b888ba8320merge master -Dorg -Ssuccess-onlyeditZarrReadereditbioformatseditbio-formats-exampleseditome-common-javaeditome-codecseditome-jaieditome-poieditbio-formats-documentationeditome-metakiteditome-stubseditome-modeledit.gitmoduleseditome-mdbtoolsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop45https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/45/Started by upstream project "Trigger" build number 5252Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue44c5cf536f21c7062363f54adfc6f66c9e248f0903c5cf536f21c7062363f54adfc6f66c9e248f0903origin/merge_cic5cf536f21c7062363f54adfc6f66c9e248f0903c5cf536f21c7062363f54adfc6f66c9e248f0903origin/merge_cic5cf536f21c7062363f54adfc6f66c9e248f0903c5cf536f21c7062363f54adfc6f66c9e248f0903origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#44474272626729BIOFORMATS-build #4444falsefalse441304SUCCESS1786406911054https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/44/testintegration2d3bc36958f07ab1b30ed192bb9e72d809ac98ba1786406474000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#67 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/67/) 2026-08-11 00:01:14 +00002d3bc36958f07ab1b30ed192bb9e72d809ac98bamerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitc5cf536f21c7062363f54adfc6f66c9e248f09031786406846000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Excluded PRs: - PR 483 melissalinkert 'Add section on deprecated API' (label: exclude) Updating db99c10d..f5e5c947 Previously merged: - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' (label: exclude) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..61116e46d3 Previously merged: - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#67 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/67/) 2026-08-11 00:07:26 +0000c5cf536f21c7062363f54adfc6f66c9e248f0903merge master -Dorg -Ssuccess-onlyeditome-common-javaeditbio-formats-exampleseditome-jaieditZarrReadereditome-modeleditome-metakiteditome-mdbtoolseditbio-formats-documentationeditome-stubseditome-poiedit.gitmoduleseditome-codecseditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop44https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/44/Started by upstream project "Trigger" build number 5151Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue4329d704e616644727e32226f662b0e9d5fc81f70029d704e616644727e32226f662b0e9d5fc81f700origin/merge_ci29d704e616644727e32226f662b0e9d5fc81f70029d704e616644727e32226f662b0e9d5fc81f700origin/merge_ci29d704e616644727e32226f662b0e9d5fc81f70029d704e616644727e32226f662b0e9d5fc81f700origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#43459481626729BIOFORMATS-build #4343falsefalse431260SUCCESS1786320452734https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/43/testintegration5aae63e639188bbc5f4c6116b9e545e74b51a4371786320074000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#66 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/66/) 2026-08-10 00:01:14 +00005aae63e639188bbc5f4c6116b9e545e74b51a437merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit29d704e616644727e32226f662b0e9d5fc81f7001786320391000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..f5e5c947 Previously merged: - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' (label: exclude) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..61116e46d3 Previously merged: - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#66 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/66/) 2026-08-10 00:06:31 +000029d704e616644727e32226f662b0e9d5fc81f700merge master -Dorg -Ssuccess-onlyeditome-metakiteditZarrReadereditbio-formats-exampleseditome-stubseditome-jaiedit.gitmoduleseditbio-formats-documentationeditome-poieditome-modeleditome-common-javaeditome-mdbtoolseditbioformatseditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop43https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/43/Started by upstream project "Trigger" build number 5050Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue4236e3beba007496f2eca3578ef3e9b1410864afc036e3beba007496f2eca3578ef3e9b1410864afc0origin/merge_ci36e3beba007496f2eca3578ef3e9b1410864afc036e3beba007496f2eca3578ef3e9b1410864afc0origin/merge_ci36e3beba007496f2eca3578ef3e9b1410864afc036e3beba007496f2eca3578ef3e9b1410864afc0origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#42464382626729BIOFORMATS-build #4242falsefalse421216SUCCESS1786234058504https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/42/testintegrationa1a6e99bc8e4275c759c4b8f58d70ab9364df5271786233681000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#65 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/65/) 2026-08-09 00:01:21 +0000a1a6e99bc8e4275c759c4b8f58d70ab9364df527merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit36e3beba007496f2eca3578ef3e9b1410864afc01786233994000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..f5e5c947 Previously merged: - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' (label: exclude) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..61116e46d3 Previously merged: - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#65 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/65/) 2026-08-09 00:06:34 +000036e3beba007496f2eca3578ef3e9b1410864afc0merge master -Dorg -Ssuccess-onlyeditome-codecseditome-jaieditome-mdbtoolseditome-poieditbio-formats-documentationeditome-common-javaeditZarrReadereditome-modeleditome-stubsedit.gitmoduleseditbio-formats-exampleseditbioformatseditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop42https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/42/Started by upstream project "Trigger" build number 4949Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue4157e62c88a950f1a0571e0ae20b8494e01d0cd5c657e62c88a950f1a0571e0ae20b8494e01d0cd5c6origin/merge_ci57e62c88a950f1a0571e0ae20b8494e01d0cd5c657e62c88a950f1a0571e0ae20b8494e01d0cd5c6origin/merge_ci57e62c88a950f1a0571e0ae20b8494e01d0cd5c657e62c88a950f1a0571e0ae20b8494e01d0cd5c6origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#41468845626729BIOFORMATS-build #4141falsefalse411172SUCCESS1786147646587https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/41/testintegration48e148e9782defa84bb2d6d6d339d45f56080a2c1786147265000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#64 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/64/) 2026-08-08 00:01:05 +000048e148e9782defa84bb2d6d6d339d45f56080a2cmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit57e62c88a950f1a0571e0ae20b8494e01d0cd5c61786147584000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..f5e5c947 Previously merged: - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' (label: exclude) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..61116e46d3 Previously merged: - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#64 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/64/) 2026-08-08 00:06:24 +000057e62c88a950f1a0571e0ae20b8494e01d0cd5c6merge master -Dorg -Ssuccess-onlyeditome-codecseditome-poieditome-metakiteditome-mdbtoolseditome-common-javaeditZarrReadereditome-modeleditome-jaieditbio-formats-exampleseditbio-formats-documentationedit.gitmoduleseditbioformatseditome-stubsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop41https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/41/Started by upstream project "Trigger" build number 4848Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue406e71bbcbea234823b8a053c1d967f8000d90ccc06e71bbcbea234823b8a053c1d967f8000d90ccc0origin/merge_ci6e71bbcbea234823b8a053c1d967f8000d90ccc06e71bbcbea234823b8a053c1d967f8000d90ccc0origin/merge_ci6e71bbcbea234823b8a053c1d967f8000d90ccc06e71bbcbea234823b8a053c1d967f8000d90ccc0origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#40452634626729BIOFORMATS-build #4040falsefalse401128SUCCESS1786103195533https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/40/testintegrationc912ec448bf278f4ef2a178a1484cc93ad59113b1786102813000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#63 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/63/) 2026-08-07 11:40:13 +0000c912ec448bf278f4ef2a178a1484cc93ad59113bmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit6e71bbcbea234823b8a053c1d967f8000d90ccc01786103131000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..f5e5c947 Previously merged: - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4464 Darlokt 'Memoizer fixes' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4457 ebenolson 'NDPI: Add writer support' (user: ebenolson) - PR 4450 Darlokt 'New CV7000 reader' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' (label: exclude) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..61116e46d3 Previously merged: - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 235 Darlokt 'Add dependabot' (user: Darlokt) - PR 234 Darlokt 'Python cleanup' (user: Darlokt) - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..1957bd78 Previously merged: - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#63 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/63/) 2026-08-07 11:45:31 +00006e71bbcbea234823b8a053c1d967f8000d90ccc0merge master -Dorg -Ssuccess-onlyeditome-metakiteditome-common-javaeditome-jaiedit.gitmoduleseditZarrReadereditome-poieditbio-formats-exampleseditome-codecseditome-mdbtoolseditbio-formats-documentationeditome-stubseditbioformatseditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop40https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/40/Started by upstream project "Trigger" build number 4747Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue395b5f3a239078cc812d8cdb6004912d43f65ee8745b5f3a239078cc812d8cdb6004912d43f65ee874origin/merge_ci5b5f3a239078cc812d8cdb6004912d43f65ee8745b5f3a239078cc812d8cdb6004912d43f65ee874origin/merge_ci5b5f3a239078cc812d8cdb6004912d43f65ee8745b5f3a239078cc812d8cdb6004912d43f65ee874origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#39463554626729BIOFORMATS-build #3939falsefalse391081SUCCESS1786061273745https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/39/testintegration654f280a08a90404266fafaefd7f4ee083a2d0171786060872000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#62 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/62/) 2026-08-07 00:01:12 +0000654f280a08a90404266fafaefd7f4ee083a2d017merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit5b5f3a239078cc812d8cdb6004912d43f65ee8741786061201000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..f5e5c947 Previously merged: - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4464 Darlokt 'Memoizer fixes' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4457 ebenolson 'NDPI: Add writer support' (user: ebenolson) - PR 4450 Darlokt 'New CV7000 reader' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' (label: exclude) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..61116e46d3 Previously merged: - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 235 Darlokt 'Add dependabot' (user: Darlokt) - PR 234 Darlokt 'Python cleanup' (user: Darlokt) - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..1957bd78 Previously merged: - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#62 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/62/) 2026-08-07 00:06:41 +00005b5f3a239078cc812d8cdb6004912d43f65ee874merge master -Dorg -Ssuccess-onlyeditome-common-javaeditome-mdbtoolseditbio-formats-exampleseditZarrReadereditbio-formats-documentationeditome-poieditbioformatseditome-metakiteditome-codecsedit.gitmoduleseditome-jaieditome-modeleditome-stubsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop39https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/39/Started by upstream project "Trigger" build number 4646Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue38839397a0c63f39867367875f82abd423205288a7839397a0c63f39867367875f82abd423205288a7origin/merge_ci839397a0c63f39867367875f82abd423205288a7839397a0c63f39867367875f82abd423205288a7origin/merge_ci839397a0c63f39867367875f82abd423205288a7839397a0c63f39867367875f82abd423205288a7origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#38453145626729BIOFORMATS-build #3838falsefalse381037SUCCESS1785974861827https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/38/testintegrationd996dc9275dc8eac16b28ffb88afec21fe5afa6d1785974478000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#61 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/61/) 2026-08-06 00:01:18 +0000d996dc9275dc8eac16b28ffb88afec21fe5afa6dmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit839397a0c63f39867367875f82abd423205288a71785974799000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..f5e5c947 Previously merged: - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'Formats bsd test resource cleanup fix' (user: Darlokt) - PR 4464 Darlokt 'Memoizer fixes' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4457 ebenolson 'NDPI: Add writer support' (user: ebenolson) - PR 4450 Darlokt 'New CV7000 reader' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' (label: exclude) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..61116e46d3 Previously merged: - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 235 Darlokt 'Add dependabot' (user: Darlokt) - PR 234 Darlokt 'Python cleanup' (user: Darlokt) - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..1957bd78 Previously merged: - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#61 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/61/) 2026-08-06 00:06:39 +0000839397a0c63f39867367875f82abd423205288a7merge master -Dorg -Ssuccess-onlyeditZarrReadereditome-metakiteditome-stubseditbio-formats-documentationeditome-poieditome-modeleditome-codecseditbio-formats-exampleseditome-mdbtoolseditome-jaieditbioformatseditome-common-javaedit.gitmodulesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop38https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/38/Started by upstream project "Trigger" build number 4545Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue37998240446b12c9685f4d24c58a63b3396e3e6e5d998240446b12c9685f4d24c58a63b3396e3e6e5dorigin/merge_ci998240446b12c9685f4d24c58a63b3396e3e6e5d998240446b12c9685f4d24c58a63b3396e3e6e5dorigin/merge_ci998240446b12c9685f4d24c58a63b3396e3e6e5d998240446b12c9685f4d24c58a63b3396e3e6e5dorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#37595488626729BIOFORMATS-build #3737falsefalse37993SUCCESS1785888454813https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/37/testintegration0118ec34a9263e5c6d3edf1e357ad2ef1df9d79a1785888080000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#60 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/60/) 2026-08-05 00:01:20 +00000118ec34a9263e5c6d3edf1e357ad2ef1df9d79amerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit998240446b12c9685f4d24c58a63b3396e3e6e5d1785888396000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..f5e5c947 Previously merged: - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4464 Darlokt 'Memoizer fixes' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4457 ebenolson 'NDPI: Add writer support' (user: ebenolson) - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..f9a0ce2765 Previously merged: - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 235 Darlokt 'Add dependabot' (user: Darlokt) - PR 234 Darlokt 'Python cleanup' (user: Darlokt) - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..1957bd78 Previously merged: - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#60 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/60/) 2026-08-05 00:06:36 +0000998240446b12c9685f4d24c58a63b3396e3e6e5dmerge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditome-modeleditZarrReadereditome-codecseditbio-formats-exampleseditome-common-javaeditbioformatseditome-jaieditome-metakiteditome-poiedit.gitmoduleseditome-stubseditome-mdbtoolsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop37https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/37/Started by upstream project "Trigger" build number 4444Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue361390b2a6d780dfcbd8127b6da02ad5344316fdc31390b2a6d780dfcbd8127b6da02ad5344316fdc3origin/merge_ci1390b2a6d780dfcbd8127b6da02ad5344316fdc31390b2a6d780dfcbd8127b6da02ad5344316fdc3origin/merge_ci1390b2a6d780dfcbd8127b6da02ad5344316fdc31390b2a6d780dfcbd8127b6da02ad5344316fdc3origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#36435916626729BIOFORMATS-build #3636falsefalse36944SUCCESS1785802047162https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/36/testintegration30170eb8a1f2330d75242aa02f3b0834990dd2981785801674000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#58 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/58/) 2026-08-04 00:01:14 +000030170eb8a1f2330d75242aa02f3b0834990dd298merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit1390b2a6d780dfcbd8127b6da02ad5344316fdc31785801987000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..f5e5c947 Previously merged: - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4464 Darlokt 'Memoizer fixes' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4457 ebenolson 'NDPI: Add writer support' (user: ebenolson) - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..f9a0ce2765 Previously merged: - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..1957bd78 Previously merged: - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#58 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/58/) 2026-08-04 00:06:27 +00001390b2a6d780dfcbd8127b6da02ad5344316fdc3merge master -Dorg -Ssuccess-onlyeditome-modeleditome-mdbtoolseditome-codecsedit.gitmoduleseditome-common-javaeditome-stubseditbio-formats-documentationeditbio-formats-exampleseditbioformatseditZarrReadereditome-poieditome-metakiteditome-jaigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop36https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/36/Started by upstream project "Trigger" build number 4343Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue35f89cf943b5380ec5ef5a973079d3fd88c6b2bb7ff89cf943b5380ec5ef5a973079d3fd88c6b2bb7forigin/merge_cif89cf943b5380ec5ef5a973079d3fd88c6b2bb7ff89cf943b5380ec5ef5a973079d3fd88c6b2bb7forigin/merge_cif89cf943b5380ec5ef5a973079d3fd88c6b2bb7ff89cf943b5380ec5ef5a973079d3fd88c6b2bb7forigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#35435302626729BIOFORMATS-build #3535falsefalse35893SUCCESS1785715645145https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/35/testintegration29812db8b4cf9b092769d6edce816cb222927b591785715278000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#57 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/57/) 2026-08-03 00:01:18 +000029812db8b4cf9b092769d6edce816cb222927b59merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitf89cf943b5380ec5ef5a973079d3fd88c6b2bb7f1785715587000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..12f8e6bc Previously merged: - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4464 Darlokt 'Memoizer fixes' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4457 ebenolson 'NDPI: Add writer support' (user: ebenolson) - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..f9a0ce2765 Previously merged: - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..1957bd78 Previously merged: - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#57 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/57/) 2026-08-03 00:06:27 +0000f89cf943b5380ec5ef5a973079d3fd88c6b2bb7fmerge master -Dorg -Ssuccess-onlyeditbioformatseditome-poieditbio-formats-documentationeditome-mdbtoolsedit.gitmoduleseditbio-formats-exampleseditZarrReadereditome-common-javaeditome-codecseditome-metakiteditome-jaieditome-stubseditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop35https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/35/Started by upstream project "Trigger" build number 4242Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue341e41bde2e17e3b5a4306a545656b51693a0f60831e41bde2e17e3b5a4306a545656b51693a0f6083origin/merge_ci1e41bde2e17e3b5a4306a545656b51693a0f60831e41bde2e17e3b5a4306a545656b51693a0f6083origin/merge_ci1e41bde2e17e3b5a4306a545656b51693a0f60831e41bde2e17e3b5a4306a545656b51693a0f6083origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#34480102626729BIOFORMATS-build #3434falsefalse34849SUCCESS1785657531064https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/34/testintegration8b20f4859c90ece02f9a31cb2a3e3f83007b07e61785657175000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#56 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/56/) 2026-08-02 07:52:55 +00008b20f4859c90ece02f9a31cb2a3e3f83007b07e6merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit1e41bde2e17e3b5a4306a545656b51693a0f60831785657464000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..12f8e6bc Previously merged: - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4464 Darlokt 'Memoizer fixes' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4457 ebenolson 'NDPI: Add writer support' (user: ebenolson) - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..f9a0ce2765 Previously merged: - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..1957bd78 Previously merged: - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#56 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/56/) 2026-08-02 07:57:44 +00001e41bde2e17e3b5a4306a545656b51693a0f6083merge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditome-jaieditZarrReadereditome-stubseditbio-formats-documentationeditome-modeleditome-mdbtoolseditome-common-javaeditbioformatsedit.gitmoduleseditome-metakiteditome-codecseditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop34https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/34/Started by upstream project "Trigger" build number 4141Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue33f1ad5633c9a08eb2b2713b2ff98fe8e8960ef171f1ad5633c9a08eb2b2713b2ff98fe8e8960ef171origin/merge_cif1ad5633c9a08eb2b2713b2ff98fe8e8960ef171f1ad5633c9a08eb2b2713b2ff98fe8e8960ef171origin/merge_cif1ad5633c9a08eb2b2713b2ff98fe8e8960ef171f1ad5633c9a08eb2b2713b2ff98fe8e8960ef171origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#33441514626729BIOFORMATS-build #3333falsefalse33805SUCCESS1785629246658https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/33/testintegration0ee3db438f0c2bace01731c9f07c43f04ff5ddce1785628877000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#55 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/55/) 2026-08-02 00:01:17 +00000ee3db438f0c2bace01731c9f07c43f04ff5ddcemerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitf1ad5633c9a08eb2b2713b2ff98fe8e8960ef1711785629187000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..12f8e6bc Previously merged: - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4464 Darlokt 'Memoizer fixes' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4457 ebenolson 'NDPI: Add writer support' (user: ebenolson) - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..f9a0ce2765 Previously merged: - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Excluded PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) Updating 3d70a1f9..1957bd78 Previously merged: - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#55 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/55/) 2026-08-02 00:06:27 +0000f1ad5633c9a08eb2b2713b2ff98fe8e8960ef171merge master -Dorg -Ssuccess-onlyeditbioformatseditome-stubseditome-metakiteditome-mdbtoolseditome-poieditome-codecseditome-modeleditome-common-javaeditZarrReadereditbio-formats-documentationedit.gitmoduleseditbio-formats-exampleseditome-jaigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop33https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/33/Started by upstream project "Trigger" build number 4040Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue32cd2813e70c774c33746499242844b6b56872667ecd2813e70c774c33746499242844b6b56872667eorigin/merge_cicd2813e70c774c33746499242844b6b56872667ecd2813e70c774c33746499242844b6b56872667eorigin/merge_cicd2813e70c774c33746499242844b6b56872667ecd2813e70c774c33746499242844b6b56872667eorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#32610507626729BIOFORMATS-build #3232falsefalse32760SUCCESS1785580721540https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/32/testintegration4ca89b9560d635f520b18ed800107f5497b1e8cb1785580361000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#54 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/54/) 2026-08-01 10:32:41 +00004ca89b9560d635f520b18ed800107f5497b1e8cbmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitcd2813e70c774c33746499242844b6b56872667e1785580661000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..12f8e6bc Previously merged: - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4457 ebenolson 'NDPI: Add writer support' (user: ebenolson) - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..f9a0ce2765 Previously merged: - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..1957bd78 Previously merged: - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#54 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/54/) 2026-08-01 10:37:41 +0000cd2813e70c774c33746499242844b6b56872667emerge master -Dorg -Ssuccess-onlyeditome-modeleditome-poieditome-stubseditome-mdbtoolseditome-metakiteditome-codecseditbio-formats-documentationeditome-common-javaeditbio-formats-examplesedit.gitmoduleseditbioformatseditome-jaieditZarrReadergithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop32https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/32/Started by upstream project "Trigger" build number 3838Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue31a2235e57dc7e95570f74d164bd51419369820e0da2235e57dc7e95570f74d164bd51419369820e0dorigin/merge_cia2235e57dc7e95570f74d164bd51419369820e0da2235e57dc7e95570f74d164bd51419369820e0dorigin/merge_cia2235e57dc7e95570f74d164bd51419369820e0da2235e57dc7e95570f74d164bd51419369820e0dorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#31454990626729BIOFORMATS-build #3131falsefalse31707SUCCESS1785456444907https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/31/testintegration48952f017a407a71448d521a0055c66a194c7eae1785456081000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#50 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/50/) 2026-07-31 00:01:21 +000048952f017a407a71448d521a0055c66a194c7eaemerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakita2235e57dc7e95570f74d164bd51419369820e0d1785456385000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..12f8e6bc Previously merged: - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4457 ebenolson 'NDPI: Add writer support' (user: ebenolson) - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..5a05d54bd3 Previously merged: - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..1957bd78 Previously merged: - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#50 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/50/) 2026-07-31 00:06:25 +0000a2235e57dc7e95570f74d164bd51419369820e0dmerge master -Dorg -Ssuccess-onlyeditome-mdbtoolseditbio-formats-documentationeditome-poieditome-jaieditome-common-javaeditome-metakiteditbioformatsedit.gitmoduleseditZarrReadereditome-codecseditome-stubseditbio-formats-exampleseditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop31https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/31/Started by upstream project "Trigger" build number 3737Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue30789b9856c6e27bb3eec0f4a72ab0a21ed37a28c5789b9856c6e27bb3eec0f4a72ab0a21ed37a28c5origin/merge_ci789b9856c6e27bb3eec0f4a72ab0a21ed37a28c5789b9856c6e27bb3eec0f4a72ab0a21ed37a28c5origin/merge_ci789b9856c6e27bb3eec0f4a72ab0a21ed37a28c5789b9856c6e27bb3eec0f4a72ab0a21ed37a28c5origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#30429984626729BIOFORMATS-build #3030falsefalse30663SUCCESS1785370067932https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/30/testintegration5994452b90599f98bdd70dbeb3d18dcd5bed54b61785369691000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#49 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/49/) 2026-07-30 00:01:31 +00005994452b90599f98bdd70dbeb3d18dcd5bed54b6merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit789b9856c6e27bb3eec0f4a72ab0a21ed37a28c51785370009000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..12f8e6bc Previously merged: - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..b486f7c4b4 Previously merged: - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#49 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/49/) 2026-07-30 00:06:49 +0000789b9856c6e27bb3eec0f4a72ab0a21ed37a28c5merge master -Dorg -Ssuccess-onlyeditome-mdbtoolsedit.gitmoduleseditome-common-javaeditome-poieditome-jaieditbioformatseditome-codecseditbio-formats-documentationeditZarrReadereditbio-formats-exampleseditome-metakiteditome-stubseditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop30https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/30/Started by upstream project "Trigger" build number 3636Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue29f34448d4eb73ee1f4bbfc8d1d3d2c213960a7ab5f34448d4eb73ee1f4bbfc8d1d3d2c213960a7ab5origin/merge_cif34448d4eb73ee1f4bbfc8d1d3d2c213960a7ab5f34448d4eb73ee1f4bbfc8d1d3d2c213960a7ab5origin/merge_cif34448d4eb73ee1f4bbfc8d1d3d2c213960a7ab5f34448d4eb73ee1f4bbfc8d1d3d2c213960a7ab5origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#29551538626729BIOFORMATS-build #2929falsefalse29612SUCCESS1785325421786https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/29/testintegrationc574df04a29cb64905e17370a0cf32d1c6bcf6ec1785325062000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#48 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/48/) 2026-07-29 11:37:42 +0000c574df04a29cb64905e17370a0cf32d1c6bcf6ecmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitf34448d4eb73ee1f4bbfc8d1d3d2c213960a7ab51785325363000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..12f8e6bc Previously merged: - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..b486f7c4b4 Previously merged: - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..3d2f042 Previously merged: - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' Conflicting PRs (not included): - PR 118 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.18.9' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#48 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/48/) 2026-07-29 11:42:43 +0000f34448d4eb73ee1f4bbfc8d1d3d2c213960a7ab5merge master -Dorg -Ssuccess-onlyeditome-common-javaeditome-jaieditome-modeleditome-poieditZarrReadereditome-codecseditome-metakiteditome-stubseditbio-formats-examplesedit.gitmoduleseditome-mdbtoolseditbio-formats-documentationeditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop29https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/29/Started by upstream project "Trigger" build number 3434Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue28831235ddc989f534c60e87bed66b35704c84aec5831235ddc989f534c60e87bed66b35704c84aec5origin/merge_ci831235ddc989f534c60e87bed66b35704c84aec5831235ddc989f534c60e87bed66b35704c84aec5origin/merge_ci831235ddc989f534c60e87bed66b35704c84aec5831235ddc989f534c60e87bed66b35704c84aec5origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#28577434626729BIOFORMATS-build #2828falsefalse28546SUCCESS1785244068705https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/28/testintegration66f1a6700d011a67bbb0900dae71e33a1ec291431785243668000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#42 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/42/) 2026-07-28 13:01:08 +000066f1a6700d011a67bbb0900dae71e33a1ec29143merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit831235ddc989f534c60e87bed66b35704c84aec51785244005000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..12f8e6bc Previously merged: - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..b486f7c4b4 Previously merged: - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' Conflicting PRs (not included): - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#42 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/42/) 2026-07-28 13:06:45 +0000831235ddc989f534c60e87bed66b35704c84aec5merge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditome-mdbtoolseditome-common-javaedit.gitmoduleseditome-codecseditbio-formats-exampleseditbioformatseditome-modeleditome-jaieditome-metakiteditome-stubseditZarrReadereditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop28https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/28/Started by upstream project "Trigger" build number 3131Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue27265f2da39559c56213e0a9e0164f41736e3017ed265f2da39559c56213e0a9e0164f41736e3017edorigin/merge_ci265f2da39559c56213e0a9e0164f41736e3017ed265f2da39559c56213e0a9e0164f41736e3017edorigin/merge_ci265f2da39559c56213e0a9e0164f41736e3017ed265f2da39559c56213e0a9e0164f41736e3017edorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#27448112626729BIOFORMATS-build #2727falsefalse27495SUCCESS1785110857907https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/27/testintegrationfc4a4c9014186586000e5b7d9a13dd96903c1ab21785110476000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#41 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/41/) 2026-07-27 00:01:16 +0000fc4a4c9014186586000e5b7d9a13dd96903c1ab2merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit265f2da39559c56213e0a9e0164f41736e3017ed1785110802000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..a9bbcc32 Previously merged: - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..b486f7c4b4 Previously merged: - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#41 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/41/) 2026-07-27 00:06:42 +0000265f2da39559c56213e0a9e0164f41736e3017edmerge master -Dorg -Ssuccess-onlyeditome-metakiteditome-common-javaeditbioformatseditome-codecseditome-poieditome-modeleditbio-formats-documentationeditome-jaieditome-mdbtoolseditome-stubseditbio-formats-exampleseditZarrReaderedit.gitmodulesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop27https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/27/Started by upstream project "Trigger" build number 3030Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue26906c4d72b69e1aaad611a8ab2f40668ba2ad04aa906c4d72b69e1aaad611a8ab2f40668ba2ad04aaorigin/merge_ci906c4d72b69e1aaad611a8ab2f40668ba2ad04aa906c4d72b69e1aaad611a8ab2f40668ba2ad04aaorigin/merge_ci906c4d72b69e1aaad611a8ab2f40668ba2ad04aa906c4d72b69e1aaad611a8ab2f40668ba2ad04aaorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#26460237626729BIOFORMATS-build #2626falsefalse26451SUCCESS1785024465806https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/26/testintegrationcd83788b4ea63dd41f9958403dadb38042c3e3f41785024078000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#40 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/40/) 2026-07-26 00:01:18 +0000cd83788b4ea63dd41f9958403dadb38042c3e3f4merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit906c4d72b69e1aaad611a8ab2f40668ba2ad04aa1785024403000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..a9bbcc32 Previously merged: - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..b486f7c4b4 Previously merged: - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#40 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/40/) 2026-07-26 00:06:43 +0000906c4d72b69e1aaad611a8ab2f40668ba2ad04aamerge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditome-poieditbio-formats-documentationeditome-jaieditome-common-javaeditZarrReadereditbioformatseditome-metakitedit.gitmoduleseditome-stubseditome-codecseditome-mdbtoolseditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop26https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/26/Started by upstream project "Trigger" build number 2929Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue255cb19f1d7e0ce1506b52140558187eb39792c6a45cb19f1d7e0ce1506b52140558187eb39792c6a4origin/merge_ci5cb19f1d7e0ce1506b52140558187eb39792c6a45cb19f1d7e0ce1506b52140558187eb39792c6a4origin/merge_ci5cb19f1d7e0ce1506b52140558187eb39792c6a45cb19f1d7e0ce1506b52140558187eb39792c6a4origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#25466148626729BIOFORMATS-build #2525falsefalse25407SUCCESS1784938053789https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/25/testintegratione3d284428f1d2ba5fcea32d48100ce1dd6fb31ad1784937675000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#39 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/39/) 2026-07-25 00:01:15 +0000e3d284428f1d2ba5fcea32d48100ce1dd6fb31admerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit5cb19f1d7e0ce1506b52140558187eb39792c6a41784937993000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..a9bbcc32 Previously merged: - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..b486f7c4b4 Previously merged: - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#39 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/39/) 2026-07-25 00:06:33 +00005cb19f1d7e0ce1506b52140558187eb39792c6a4merge master -Dorg -Ssuccess-onlyeditome-metakiteditome-jaieditome-stubseditome-modeledit.gitmoduleseditbioformatseditome-codecseditome-poieditbio-formats-documentationeditbio-formats-exampleseditome-mdbtoolseditZarrReadereditome-common-javagithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop25https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/25/Started by upstream project "Trigger" build number 2828Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue2474f853514947a38d7eb7cf6481791ce4596c713374f853514947a38d7eb7cf6481791ce4596c7133origin/merge_ci74f853514947a38d7eb7cf6481791ce4596c713374f853514947a38d7eb7cf6481791ce4596c7133origin/merge_ci74f853514947a38d7eb7cf6481791ce4596c713374f853514947a38d7eb7cf6481791ce4596c7133origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#24485294626729BIOFORMATS-build #2424falsefalse24363SUCCESS1784851661880https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/24/testintegration1a72d49caf324d214716460958ef393b69c04d301784851279000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#38 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/38/) 2026-07-24 00:01:19 +00001a72d49caf324d214716460958ef393b69c04d30merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit74f853514947a38d7eb7cf6481791ce4596c71331784851604000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..a9bbcc32 Previously merged: - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..b486f7c4b4 Previously merged: - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#38 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/38/) 2026-07-24 00:06:44 +000074f853514947a38d7eb7cf6481791ce4596c7133merge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditome-mdbtoolseditbioformatseditome-jaieditome-codecseditome-metakiteditome-modeleditome-stubseditZarrReadereditbio-formats-documentationeditome-common-javaeditome-poiedit.gitmodulesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop24https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/24/Started by upstream project "Trigger" build number 2727Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue238ec86f061ec5b1affb8f798bc4b9c088b33bcde88ec86f061ec5b1affb8f798bc4b9c088b33bcde8origin/merge_ci8ec86f061ec5b1affb8f798bc4b9c088b33bcde88ec86f061ec5b1affb8f798bc4b9c088b33bcde8origin/merge_ci8ec86f061ec5b1affb8f798bc4b9c088b33bcde88ec86f061ec5b1affb8f798bc4b9c088b33bcde8origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#23447359626729BIOFORMATS-build #2323falsefalse23319SUCCESS1784765249920https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/23/testintegration245f594296856b17191ba886ad5aedfad34036b01784764872000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#37 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/37/) 2026-07-23 00:01:12 +0000245f594296856b17191ba886ad5aedfad34036b0merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit8ec86f061ec5b1affb8f798bc4b9c088b33bcde81784765191000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..a9bbcc32 Previously merged: - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..b486f7c4b4 Previously merged: - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#37 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/37/) 2026-07-23 00:06:31 +00008ec86f061ec5b1affb8f798bc4b9c088b33bcde8merge master -Dorg -Ssuccess-onlyeditZarrReaderedit.gitmoduleseditome-jaieditome-codecseditome-stubseditome-metakiteditome-poieditbio-formats-exampleseditbioformatseditome-modeleditome-mdbtoolseditome-common-javaeditbio-formats-documentationgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop23https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/23/Started by upstream project "Trigger" build number 2626Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue22e8cea1dba0ab458cbc5e918a63f9069c9c9cc65ee8cea1dba0ab458cbc5e918a63f9069c9c9cc65eorigin/merge_cie8cea1dba0ab458cbc5e918a63f9069c9c9cc65ee8cea1dba0ab458cbc5e918a63f9069c9c9cc65eorigin/merge_cie8cea1dba0ab458cbc5e918a63f9069c9c9cc65ee8cea1dba0ab458cbc5e918a63f9069c9c9cc65eorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#22542800626729BIOFORMATS-build #2222falsefalse22275SUCCESS1784717688939https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/22/testintegrationd16327568962f5dc37b6d5bb7f8d06bde26591981784717311000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#36 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/36/) 2026-07-22 10:48:31 +0000d16327568962f5dc37b6d5bb7f8d06bde2659198merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakite8cea1dba0ab458cbc5e918a63f9069c9c9cc65e1784717628000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..a9bbcc32 Previously merged: - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..b486f7c4b4 Previously merged: - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#36 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/36/) 2026-07-22 10:53:48 +0000e8cea1dba0ab458cbc5e918a63f9069c9c9cc65emerge master -Dorg -Ssuccess-onlyeditome-modeleditbio-formats-exampleseditbio-formats-documentationedit.gitmoduleseditome-common-javaeditome-jaieditbioformatseditome-mdbtoolseditome-metakiteditome-poieditZarrReadereditome-codecseditome-stubsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop22https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/22/Started by upstream project "Trigger" build number 2424Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue219a04ac44306530cbea4eed8ce96bc73e526aaadc9a04ac44306530cbea4eed8ce96bc73e526aaadcorigin/merge_ci9a04ac44306530cbea4eed8ce96bc73e526aaadc9a04ac44306530cbea4eed8ce96bc73e526aaadcorigin/merge_ci9a04ac44306530cbea4eed8ce96bc73e526aaadc9a04ac44306530cbea4eed8ce96bc73e526aaadcorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#21446420626729BIOFORMATS-build #2121falsefalse21209SUCCESS1784592470352https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/21/testintegration4a2eed50d51466b5cc6c9d1732a48ca5791bcc5d1784592084000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#35 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/35/) 2026-07-21 00:01:24 +00004a2eed50d51466b5cc6c9d1732a48ca5791bcc5dmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit9a04ac44306530cbea4eed8ce96bc73e526aaadc1784592408000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..a9bbcc32 Previously merged: - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#35 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/35/) 2026-07-21 00:06:48 +00009a04ac44306530cbea4eed8ce96bc73e526aaadcmerge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditbioformatseditome-jaieditZarrReadereditome-modeleditome-codecseditome-metakiteditome-mdbtoolsedit.gitmoduleseditome-stubseditome-poieditbio-formats-documentationeditome-common-javagithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop21https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/21/Started by upstream project "Trigger" build number 2323Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue20d958d5f126d0779e3b072a3cff1e7e56b3645c28d958d5f126d0779e3b072a3cff1e7e56b3645c28origin/merge_cid958d5f126d0779e3b072a3cff1e7e56b3645c28d958d5f126d0779e3b072a3cff1e7e56b3645c28origin/merge_cid958d5f126d0779e3b072a3cff1e7e56b3645c28d958d5f126d0779e3b072a3cff1e7e56b3645c28origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#20520738626729BIOFORMATS-build #2020falsefalse20165SUCCESS1784536514117https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/20/testintegrationeb948dc502409d8e842d57505b4fbdd40322a6951784536164000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#34 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/34/) 2026-07-20 08:29:24 +0000eb948dc502409d8e842d57505b4fbdd40322a695merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitd958d5f126d0779e3b072a3cff1e7e56b3645c281784536459000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..a9bbcc32 Previously merged: - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' (status: action_required) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#34 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/34/) 2026-07-20 08:34:19 +0000d958d5f126d0779e3b072a3cff1e7e56b3645c28merge master -Dorg -Ssuccess-onlyeditbioformatseditZarrReadereditome-stubseditome-common-javaedit.gitmoduleseditome-poieditome-jaieditome-modeleditbio-formats-exampleseditome-mdbtoolseditome-metakiteditbio-formats-documentationeditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop20https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/20/Started by upstream project "Trigger" build number 2121Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue192fdfce74df4b02f988fc2165a5c88573e06131892fdfce74df4b02f988fc2165a5c88573e0613189origin/merge_ci2fdfce74df4b02f988fc2165a5c88573e06131892fdfce74df4b02f988fc2165a5c88573e0613189origin/merge_ci2fdfce74df4b02f988fc2165a5c88573e06131892fdfce74df4b02f988fc2165a5c88573e0613189origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#19619492626729BIOFORMATS-build #1919falsefalse19117SUCCESS1784419651538https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/19/testintegratione3b37dde5d711a2b94ba9734bbaa6a3d61a840681784419279000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#31 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/31/) 2026-07-19 00:01:19 +0000e3b37dde5d711a2b94ba9734bbaa6a3d61a84068merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit2fdfce74df4b02f988fc2165a5c88573e06131891784419593000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..a9bbcc32 Previously merged: - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' (status: action_required) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#31 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/31/) 2026-07-19 00:06:33 +00002fdfce74df4b02f988fc2165a5c88573e0613189merge master -Dorg -Ssuccess-onlyeditome-modeleditbio-formats-exampleseditZarrReadereditome-mdbtoolseditome-metakiteditome-poieditbio-formats-documentationedit.gitmoduleseditome-codecseditome-jaieditbioformatseditome-common-javaeditome-stubsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop19https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/19/Started by upstream project "Trigger" build number 2020Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue18cecc40b71b35b31a9b7bee29e4b2b84dfa0d6aafcecc40b71b35b31a9b7bee29e4b2b84dfa0d6aaforigin/merge_cicecc40b71b35b31a9b7bee29e4b2b84dfa0d6aafcecc40b71b35b31a9b7bee29e4b2b84dfa0d6aaforigin/merge_cicecc40b71b35b31a9b7bee29e4b2b84dfa0d6aafcecc40b71b35b31a9b7bee29e4b2b84dfa0d6aaforigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#18490183626729BIOFORMATS-build #1818falsefalse1873SUCCESS1784333264596https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/18/testintegration8d8dab5b0e2820950c2d0849cd2d0ad10d1de6cd1784332876000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#30 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/30/) 2026-07-18 00:01:16 +00008d8dab5b0e2820950c2d0849cd2d0ad10d1de6cdmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitcecc40b71b35b31a9b7bee29e4b2b84dfa0d6aaf1784333207000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..a9bbcc32 Previously merged: - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#30 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/30/) 2026-07-18 00:06:47 +0000cecc40b71b35b31a9b7bee29e4b2b84dfa0d6aafmerge master -Dorg -Ssuccess-onlyeditome-modeledit.gitmoduleseditbio-formats-exampleseditome-mdbtoolseditbio-formats-documentationeditome-jaieditZarrReadereditome-codecseditome-common-javaeditbioformatseditome-stubseditome-metakiteditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop18https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/18/Started by upstream project "Trigger" build number 1818Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue173110d7046bfcc18a1e1487bc195dbd1d95598bec3110d7046bfcc18a1e1487bc195dbd1d95598becorigin/merge_ci3110d7046bfcc18a1e1487bc195dbd1d95598bec3110d7046bfcc18a1e1487bc195dbd1d95598becorigin/merge_ci3110d7046bfcc18a1e1487bc195dbd1d95598bec3110d7046bfcc18a1e1487bc195dbd1d95598becorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#17405768626729BIOFORMATS-build #1717falsefalse1723SUCCESS1784197564418https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/17/testintegration39a8cb6f6d695bfe6a1d2d3f412b7c3624ce75d11784197181000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#27 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/27/) 2026-07-16 10:19:41 +000039a8cb6f6d695bfe6a1d2d3f412b7c3624ce75d1merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit3110d7046bfcc18a1e1487bc195dbd1d95598bec1784197505000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..a9bbcc32 Previously merged: - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4453 kasper-cancilico 'Add reader for PreciPoint .vmic whole-slide images' (user: kasper-cancilico) - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#27 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/27/) 2026-07-16 10:25:05 +00003110d7046bfcc18a1e1487bc195dbd1d95598becmerge master -Dorg -Ssuccess-onlyeditome-jaieditbioformatseditome-metakiteditome-stubseditome-mdbtoolseditbio-formats-exampleseditbio-formats-documentationeditome-codecseditome-poiedit.gitmoduleseditZarrReadereditome-common-javaeditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop17https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/17/Started by upstream project "Trigger" build number 1717Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue168718ccf5c033534a8ba51cca7f3c84bd14abd7008718ccf5c033534a8ba51cca7f3c84bd14abd700origin/merge_ci8718ccf5c033534a8ba51cca7f3c84bd14abd7008718ccf5c033534a8ba51cca7f3c84bd14abd700origin/merge_ci8718ccf5c033534a8ba51cca7f3c84bd14abd7008718ccf5c033534a8ba51cca7f3c84bd14abd700origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#16512261626729BIOFORMATS-build #1616falsefalse164SUCCESS1784192519268https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/16/testintegrationf2e51628e589332e1debe4506165c3b6c989fdd91784192133000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#26 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/26/) 2026-07-16 08:55:33 +0000f2e51628e589332e1debe4506165c3b6c989fdd9merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit8718ccf5c033534a8ba51cca7f3c84bd14abd7001784192458000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..a9bbcc32 Previously merged: - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4453 kasper-cancilico 'Add reader for PreciPoint .vmic whole-slide images' (user: kasper-cancilico) - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#26 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/26/) 2026-07-16 09:00:58 +00008718ccf5c033534a8ba51cca7f3c84bd14abd700merge master -Dorg -Ssuccess-onlyeditome-jaieditome-modeleditbioformatseditome-poieditome-metakiteditome-common-javaedit.gitmoduleseditome-codecseditbio-formats-documentationeditZarrReadereditome-mdbtoolseditome-stubseditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop16https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/16/Started by upstream project "Trigger" build number 1616Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue156dc2aea500a71d7c84e35b2bf5cb3841b573cff76dc2aea500a71d7c84e35b2bf5cb3841b573cff7origin/merge_ci6dc2aea500a71d7c84e35b2bf5cb3841b573cff76dc2aea500a71d7c84e35b2bf5cb3841b573cff7origin/merge_ci6dc2aea500a71d7c84e35b2bf5cb3841b573cff76dc2aea500a71d7c84e35b2bf5cb3841b573cff7origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#15587328626729BIOFORMATS-build #1515falsefalse15522SUCCESS1784160454836https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/15/testintegrationf9ce3cba3c15f0d726763b5b37a2e5e874f47d4c1784160065000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#25 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/25/) 2026-07-16 00:01:05 +0000f9ce3cba3c15f0d726763b5b37a2e5e874f47d4cmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit6dc2aea500a71d7c84e35b2bf5cb3841b573cff71784160394000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..a9bbcc32 Previously merged: - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4453 kasper-cancilico 'Add reader for PreciPoint .vmic whole-slide images' (user: kasper-cancilico) - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#25 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/25/) 2026-07-16 00:06:34 +00006dc2aea500a71d7c84e35b2bf5cb3841b573cff7merge master -Dorg -Ssuccess-onlyeditZarrReadereditome-metakiteditome-mdbtoolseditome-poieditbio-formats-exampleseditome-modeleditbio-formats-documentationeditbioformatseditome-jaieditome-stubsedit.gitmoduleseditome-codecseditome-common-javagithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop15https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/15/Started by upstream project "Trigger" build number 1414Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue14663dd3fe9892cd073d6493c94e0ea9971e74c206663dd3fe9892cd073d6493c94e0ea9971e74c206origin/merge_ci663dd3fe9892cd073d6493c94e0ea9971e74c206663dd3fe9892cd073d6493c94e0ea9971e74c206origin/merge_ci663dd3fe9892cd073d6493c94e0ea9971e74c206663dd3fe9892cd073d6493c94e0ea9971e74c206origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#14477809626729BIOFORMATS-build #1414falsefalse14472SUCCESS1784018319769https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/14/testintegrationd6b151a304a668c6ab006f4780e65284010ef1141784017955000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#22 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/22/) 2026-07-14 08:32:35 +0000d6b151a304a668c6ab006f4780e65284010ef114merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit663dd3fe9892cd073d6493c94e0ea9971e74c2061784018262000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..a9bbcc32 Previously merged: - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#22 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/22/) 2026-07-14 08:37:42 +0000663dd3fe9892cd073d6493c94e0ea9971e74c206merge master -Dorg -Ssuccess-onlyedit.gitmoduleseditZarrReadereditome-mdbtoolseditome-modeleditome-jaieditome-common-javaeditome-codecseditbio-formats-exampleseditbio-formats-documentationeditome-metakiteditome-stubseditome-poieditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop14https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/14/Started by upstream project "Trigger" build number 1313Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue13e64b26a26ae6fffd9692b80136095535e7521cbce64b26a26ae6fffd9692b80136095535e7521cbcorigin/merge_cie64b26a26ae6fffd9692b80136095535e7521cbce64b26a26ae6fffd9692b80136095535e7521cbcorigin/merge_cie64b26a26ae6fffd9692b80136095535e7521cbce64b26a26ae6fffd9692b80136095535e7521cbcorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#13443207626729BIOFORMATS-build #1313falsefalse13466SUCCESS1783987643097https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/13/testintegration6e3e8df3ee1e8d8654d09f47bba73d7285efeaff1783987270000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#21 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/21/) 2026-07-14 00:01:10 +00006e3e8df3ee1e8d8654d09f47bba73d7285efeaffmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakite64b26a26ae6fffd9692b80136095535e7521cbc1783987584000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..a9bbcc32 Previously merged: - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#21 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/21/) 2026-07-14 00:06:24 +0000e64b26a26ae6fffd9692b80136095535e7521cbcmerge master -Dorg -Ssuccess-onlyeditome-codecsedit.gitmoduleseditome-poieditZarrReadereditome-modeleditome-metakiteditbio-formats-exampleseditome-common-javaeditome-mdbtoolseditome-stubseditome-jaieditbio-formats-documentationeditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop13https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/13/Started by upstream project "Trigger" build number 1212Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue12a8985293e6b42f17332a5f1cf2ddf7987260ac4da8985293e6b42f17332a5f1cf2ddf7987260ac4dorigin/merge_cia8985293e6b42f17332a5f1cf2ddf7987260ac4da8985293e6b42f17332a5f1cf2ddf7987260ac4dorigin/merge_cia8985293e6b42f17332a5f1cf2ddf7987260ac4da8985293e6b42f17332a5f1cf2ddf7987260ac4dorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#12444669626729BIOFORMATS-build #1212falsefalse12420SUCCESS1783901236290https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/12/testintegration4a4b222130971c9687da36e5c11a4b30345a5cf81783900873000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#20 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/20/) 2026-07-13 00:01:13 +00004a4b222130971c9687da36e5c11a4b30345a5cf8merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakita8985293e6b42f17332a5f1cf2ddf7987260ac4d1783901180000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..a9bbcc32 Previously merged: - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#20 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/20/) 2026-07-13 00:06:20 +0000a8985293e6b42f17332a5f1cf2ddf7987260ac4dmerge master -Dorg -Ssuccess-onlyeditome-codecsedit.gitmoduleseditome-modeleditZarrReadereditbio-formats-exampleseditbioformatseditbio-formats-documentationeditome-metakiteditome-mdbtoolseditome-common-javaeditome-stubseditome-jaieditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop12https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/12/Started by upstream project "Trigger" build number 1111Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue11be7f9d9124d570338384ef5eceb42acfcc1396cfbe7f9d9124d570338384ef5eceb42acfcc1396cforigin/merge_cibe7f9d9124d570338384ef5eceb42acfcc1396cfbe7f9d9124d570338384ef5eceb42acfcc1396cforigin/merge_cibe7f9d9124d570338384ef5eceb42acfcc1396cfbe7f9d9124d570338384ef5eceb42acfcc1396cforigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#11461067626729BIOFORMATS-build #1111falsefalse11376SUCCESS1783814838724https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/11/testintegration7ff92fc4e84c580cab75615d4143ccc89c2c49121783814475000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#19 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/19/) 2026-07-12 00:01:15 +00007ff92fc4e84c580cab75615d4143ccc89c2c4912merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitbe7f9d9124d570338384ef5eceb42acfcc1396cf1783814784000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..a9bbcc32 Previously merged: - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#19 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/19/) 2026-07-12 00:06:24 +0000be7f9d9124d570338384ef5eceb42acfcc1396cfmerge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditome-codecseditome-common-javaeditbio-formats-documentationeditome-mdbtoolseditZarrReadereditome-modeleditome-poieditbioformatsedit.gitmoduleseditome-metakiteditome-stubseditome-jaigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop11https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/11/Started by upstream project "Trigger" build number 1010Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue10400fbbd0de84c710bc2bc10afeb7997e41d21fa5400fbbd0de84c710bc2bc10afeb7997e41d21fa5origin/merge_ci400fbbd0de84c710bc2bc10afeb7997e41d21fa5400fbbd0de84c710bc2bc10afeb7997e41d21fa5origin/merge_ci400fbbd0de84c710bc2bc10afeb7997e41d21fa5400fbbd0de84c710bc2bc10afeb7997e41d21fa5origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#10556427626729BIOFORMATS-build #1010falsefalse10332SUCCESS1783728476904https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/10/testintegrationcd653ec7213f05b36048c06e01ebd593688254f61783728119000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#18 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/18/) 2026-07-11 00:01:59 +0000cd653ec7213f05b36048c06e01ebd593688254f6merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit400fbbd0de84c710bc2bc10afeb7997e41d21fa51783728422000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..a9bbcc32 Previously merged: - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#18 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/18/) 2026-07-11 00:07:02 +0000400fbbd0de84c710bc2bc10afeb7997e41d21fa5merge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditome-poiedit.gitmoduleseditome-modeleditome-stubseditZarrReadereditome-codecseditome-jaieditbio-formats-documentationeditome-mdbtoolseditome-metakiteditbioformatseditome-common-javagithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop10https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/10/Started by upstream project "Trigger" build number 99Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue9a8646c8bea484b8eb14e0a5b4504bb8b9053fa0ca8646c8bea484b8eb14e0a5b4504bb8b9053fa0corigin/merge_cia8646c8bea484b8eb14e0a5b4504bb8b9053fa0ca8646c8bea484b8eb14e0a5b4504bb8b9053fa0corigin/merge_cia8646c8bea484b8eb14e0a5b4504bb8b9053fa0ca8646c8bea484b8eb14e0a5b4504bb8b9053fa0corigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#9430856626729BIOFORMATS-build #99falsefalse9282SUCCESS1783642063186https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/9/testintegrationae6f43549dd3f3c11ef6fdab418645eb260d19ae1783641672000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#17 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/17/) 2026-07-10 00:01:12 +0000ae6f43549dd3f3c11ef6fdab418645eb260d19aemerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakita8646c8bea484b8eb14e0a5b4504bb8b9053fa0c1783642003000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..d7d2a272 Previously merged: - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#17 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/17/) 2026-07-10 00:06:43 +0000a8646c8bea484b8eb14e0a5b4504bb8b9053fa0cmerge master -Dorg -Ssuccess-onlyeditome-stubseditome-jaiedit.gitmoduleseditome-modeleditome-codecseditome-metakiteditome-poieditbioformatseditome-mdbtoolseditbio-formats-exampleseditZarrReadereditbio-formats-documentationeditome-common-javagithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop9https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/9/Started by upstream project "Trigger" build number 88Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue8c80f2d1a1f3c39cf728392ab1cd90527663d5a3ec80f2d1a1f3c39cf728392ab1cd90527663d5a3eorigin/merge_cic80f2d1a1f3c39cf728392ab1cd90527663d5a3ec80f2d1a1f3c39cf728392ab1cd90527663d5a3eorigin/merge_cic80f2d1a1f3c39cf728392ab1cd90527663d5a3ec80f2d1a1f3c39cf728392ab1cd90527663d5a3eorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#8456984626729BIOFORMATS-build #88falsefalse8220SUCCESS1783589481953https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/8/testintegration4673acf2ca38e5953a4446623f917bdaa3124d0f1783589087000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#16 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/16/) 2026-07-09 09:24:47 +00004673acf2ca38e5953a4446623f917bdaa3124d0fmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitc80f2d1a1f3c39cf728392ab1cd90527663d5a3e1783589413000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..f620d78e Previously merged: - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#16 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/16/) 2026-07-09 09:30:13 +0000c80f2d1a1f3c39cf728392ab1cd90527663d5a3emerge master -Dorg -Ssuccess-onlyeditome-jaieditome-stubseditome-poieditbio-formats-exampleseditome-metakiteditome-modeledit.gitmoduleseditZarrReadereditome-codecseditome-mdbtoolseditome-common-javaeditbio-formats-documentationeditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop8https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/8/Started by upstream project "Trigger" build number 77Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue7fc9a8aea56d4059b7581bb36146d8738640e49aefc9a8aea56d4059b7581bb36146d8738640e49aeorigin/merge_cifc9a8aea56d4059b7581bb36146d8738640e49aefc9a8aea56d4059b7581bb36146d8738640e49aeorigin/merge_cifc9a8aea56d4059b7581bb36146d8738640e49aefc9a8aea56d4059b7581bb36146d8738640e49aeorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#7528429626729BIOFORMATS-build #77falsefalse7210SUCCESS1783555681206https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/7/testintegration2d3db8c29bcb5056be08a381e770aea5cc57d4621783555298000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#15 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/15/) 2026-07-09 00:01:38 +00002d3db8c29bcb5056be08a381e770aea5cc57d462merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitfc9a8aea56d4059b7581bb36146d8738640e49ae1783555622000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..f620d78e Previously merged: - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#15 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/15/) 2026-07-09 00:07:02 +0000fc9a8aea56d4059b7581bb36146d8738640e49aemerge master -Dorg -Ssuccess-onlyeditbioformatseditome-metakiteditbio-formats-exampleseditome-jaieditome-poieditome-stubsedit.gitmoduleseditome-modeleditome-codecseditZarrReadereditbio-formats-documentationeditome-mdbtoolseditome-common-javagithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop7https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/7/Started by upstream project "Trigger" build number 66Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue68e4245c75acc2fc115746a792bb0663c4576cbca8e4245c75acc2fc115746a792bb0663c4576cbcaorigin/merge_ci8e4245c75acc2fc115746a792bb0663c4576cbca8e4245c75acc2fc115746a792bb0663c4576cbcaorigin/merge_ci8e4245c75acc2fc115746a792bb0663c4576cbca8e4245c75acc2fc115746a792bb0663c4576cbcaorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#6412275626729BIOFORMATS-build #66falsefalse6147SUCCESS1783469248712https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/6/testintegration6d15fe69cea02417b083e2813ac5eeaf492ce5611783468868000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#14 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/14/) 2026-07-08 00:01:08 +00006d15fe69cea02417b083e2813ac5eeaf492ce561merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit8e4245c75acc2fc115746a792bb0663c4576cbca1783469190000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..f620d78e Previously merged: - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#14 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/14/) 2026-07-08 00:06:30 +00008e4245c75acc2fc115746a792bb0663c4576cbcamerge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditbio-formats-exampleseditome-modeleditome-codecsedit.gitmoduleseditbioformatseditome-stubseditome-mdbtoolseditome-metakiteditZarrReadereditome-jaieditome-poieditome-common-javagithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop6https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/6/Started by upstream project "Trigger" build number 55Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue52f5cfd10cd114d16d1d59b29fab12c7118ee7d622f5cfd10cd114d16d1d59b29fab12c7118ee7d62origin/merge_ci2f5cfd10cd114d16d1d59b29fab12c7118ee7d622f5cfd10cd114d16d1d59b29fab12c7118ee7d62origin/merge_ci2f5cfd10cd114d16d1d59b29fab12c7118ee7d622f5cfd10cd114d16d1d59b29fab12c7118ee7d62origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#5581242626729BIOFORMATS-build #55falsefalse599SUCCESS1783421732549https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/5/testintegratione4251a74e6482c67048787d124a4e80b241578221783421380000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#13 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/13/) 2026-07-07 10:49:40 +0000e4251a74e6482c67048787d124a4e80b24157822merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit2f5cfd10cd114d16d1d59b29fab12c7118ee7d621783421677000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..f620d78e Previously merged: - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#13 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/13/) 2026-07-07 10:54:37 +00002f5cfd10cd114d16d1d59b29fab12c7118ee7d62merge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditome-metakiteditome-poieditome-stubsedit.gitmoduleseditbioformatseditome-jaieditome-common-javaeditome-modeleditome-codecseditome-mdbtoolseditZarrReadereditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop5https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/5/Started by upstream project "Trigger" build number 44Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue40fcb2408b754357e32d6ace4bebc43cced0ba35d0fcb2408b754357e32d6ace4bebc43cced0ba35dorigin/merge_ci0fcb2408b754357e32d6ace4bebc43cced0ba35d0fcb2408b754357e32d6ace4bebc43cced0ba35dorigin/merge_ci0fcb2408b754357e32d6ace4bebc43cced0ba35d0fcb2408b754357e32d6ace4bebc43cced0ba35dorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#4456197626729BIOFORMATS-build #44falsefalse475SUCCESS1783382928915https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/4/testintegration6399110079f05b183f7b9e5c0d34ed04b777f34f1783382456000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#10 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/10/) 2026-07-07 00:00:56 +00006399110079f05b183f7b9e5c0d34ed04b777f34fmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitdec1606c4b21d146383265e78ce3716f6e30752c1783382769000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..f620d78e Previously merged: - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 476 melissalinkert 'Update logback to 1.5.37' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4452 melissalinkert 'Update logback to 1.5.37' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' - PR 117 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 34 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 232 melissalinkert 'Update logback to 1.5.37' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#10 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/10/) 2026-07-07 00:06:09 +0000dec1606c4b21d146383265e78ce3716f6e30752cmerge master -Dorg -Ssuccess-onlyedit.gitmoduleseditbio-formats-documentationeditome-poieditZarrReadereditome-metakiteditome-stubseditbio-formats-exampleseditome-mdbtoolseditbioformatseditome-codecseditome-modeleditome-jaieditome-common-javabioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit0fcb2408b754357e32d6ace4bebc43cced0ba35d1783382918000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-07-07 00:08:38 +00000fcb2408b754357e32d6ace4bebc43cced0ba35dUpdate component versionseditbioformatseditome-modeleditome-codecseditome-metakiteditbio-formats-documentationeditbio-formats-exampleseditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop4https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/4/Started by upstream project "Trigger" build number 33Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue3c71805ba73148598305093dca665435e660fac2ec71805ba73148598305093dca665435e660fac2eorigin/merge_cic71805ba73148598305093dca665435e660fac2ec71805ba73148598305093dca665435e660fac2eorigin/merge_cic71805ba73148598305093dca665435e660fac2ec71805ba73148598305093dca665435e660fac2eorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#3383768626729BIOFORMATS-build #33falsefalse338SUCCESS1783348813127https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/3/testintegration61a3b6acae43bcf26041b281a5c2b4d3612b08fd1783348368000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#9 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/9/) 2026-07-06 14:32:48 +000061a3b6acae43bcf26041b281a5c2b4d3612b08fdmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitf6caf89b4eac6a07b8ee3366d81117ce29f369661783348659000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..f620d78e Previously merged: - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 475 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.5.25 to 1.5.33' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#9 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/9/) 2026-07-06 14:37:39 +0000f6caf89b4eac6a07b8ee3366d81117ce29f36966merge master -Dorg -Ssuccess-onlyeditome-mdbtoolseditbio-formats-documentationeditbioformatseditbio-formats-exampleseditome-metakiteditZarrReadereditome-common-javaeditome-jaieditome-poiedit.gitmoduleseditome-codecseditome-stubseditome-modelbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitc71805ba73148598305093dca665435e660fac2e1783348804000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-07-06 14:40:04 +0000c71805ba73148598305093dca665435e660fac2eUpdate component versionseditome-metakiteditbio-formats-exampleseditome-codecseditome-poieditbio-formats-documentationeditbioformatseditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop3https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/3/Started by upstream project "Trigger" build number 22Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue2f5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206f5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206origin/merge_cif5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206f5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206origin/merge_cif5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206f5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#2531203626729BIOFORMATS-build #22falsefalse221SUCCESS1783344847999https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/2/testintegrationdd4caa3477b204bc90b9322bed06559fef2e8b5f1783344417000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#8 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/8/) 2026-07-06 13:26:57 +0000dd4caa3477b204bc90b9322bed06559fef2e8b5fmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit8cd699c425887fb940558935ead7a3ca2d5a09241783344700000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..f620d78e Previously merged: - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 475 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.5.25 to 1.5.33' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4450 Darlokt 'Fix CV7000 sparse acquisition series and metadata handling' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..1178fa8b25 Previously merged: - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' Conflicting PRs (not included): - PR 4445 melissalinkert '.vsi fill color fixes' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..b721c0a Previously merged: - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Merged PRs: - PR 108 dominikl 'Remove S3 handling' - PR 116 dependabot[bot] 'Bump com.fasterxml.jackson.core:jackson-databind from 2.14.2 to 2.22.0' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b8b3a62 Previously merged: - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..8be3f6cb Previously merged: - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#8 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/8/) 2026-07-06 13:31:40 +00008cd699c425887fb940558935ead7a3ca2d5a0924merge master -Dorg -Ssuccess-onlyeditome-stubseditbio-formats-documentationeditome-jaieditZarrReadereditome-poieditbio-formats-exampleseditome-common-javaeditome-metakiteditome-codecseditome-mdbtoolseditome-modeledit.gitmoduleseditbioformatsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitf5303d2e5bf2bb636a2b62a9c06a85b7a0f5f2061783344836000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-07-06 13:33:56 +0000f5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206Update component versionseditbio-formats-documentationeditome-codecseditome-modeleditome-metakiteditome-poieditbio-formats-exampleseditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop2https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/2/Started by upstream project "Trigger" build number 11Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue1226ce8f736a38261ebb77afbbb119519014af811226ce8f736a38261ebb77afbbb119519014af811origin/merge_ci226ce8f736a38261ebb77afbbb119519014af811226ce8f736a38261ebb77afbbb119519014af811origin/merge_ci226ce8f736a38261ebb77afbbb119519014af811226ce8f736a38261ebb77afbbb119519014af811origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#1308458626729BIOFORMATS-build #11falsefalse116FAILURE1783343847945https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/1/testintegrationgit1https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/1/blueStarted by upstream project "Trigger" build number 11Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue1226ce8f736a38261ebb77afbbb119519014af811226ce8f736a38261ebb77afbbb119519014af811origin/merge_ci226ce8f736a38261ebb77afbbb119519014af811226ce8f736a38261ebb77afbbb119519014af811origin/merge_ci226ce8f736a38261ebb77afbbb119519014af811226ce8f736a38261ebb77afbbb119519014af811origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#1308458626729BIOFORMATS-build #11falsefalse116FAILURE1783343847945https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/1/testintegrationgit1https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/1/Build stability: No recent builds failed.icon-health-80plushealth-80plus.png100falsefalseStarted by upstream project "Trigger" build number 118118Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue100440badce7006c269044aed9d9e223062cf8940e0440badce7006c269044aed9d9e223062cf8940e0origin/merge_ci440badce7006c269044aed9d9e223062cf8940e0440badce7006c269044aed9d9e223062cf8940e0origin/merge_ci440badce7006c269044aed9d9e223062cf8940e0440badce7006c269044aed9d9e223062cf8940e0origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#100601062626729BIOFORMATS-build #100100falsefalse1003683SUCCESS1791065284122https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/100/testintegration0f56ae9e3c5d57fb5ddbe7cb8cdffaca70e83a681791064887000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#146 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/146/) 2026-10-03 22:01:27 +00000f56ae9e3c5d57fb5ddbe7cb8cdffaca70e83a68merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit440badce7006c269044aed9d9e223062cf8940e01791065216000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..cf21ea57 Previously merged: - PR 487 pwalczysko 'Gatan2' - PR 486 pwalczysko 'Exclude gatan urls: 429 too many redirects' - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..9d5baf57d7 Previously merged: - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4487 sbesson 'TiffParser: log failed endian check at DEBUG level' - PR 4486 melissalinkert 'Upgrade check cleanup' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#146 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/146/) 2026-10-03 22:06:56 +0000440badce7006c269044aed9d9e223062cf8940e0merge master -Dorg -Ssuccess-onlyeditome-poieditbio-formats-documentationeditbio-formats-exampleseditbioformatsedit.gitmoduleseditome-common-javaeditome-modeleditome-mdbtoolseditome-metakiteditome-jaieditome-codecseditZarrReadereditome-stubsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop100https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/100/Started by upstream project "Trigger" build number 118118Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue100440badce7006c269044aed9d9e223062cf8940e0440badce7006c269044aed9d9e223062cf8940e0origin/merge_ci440badce7006c269044aed9d9e223062cf8940e0440badce7006c269044aed9d9e223062cf8940e0origin/merge_ci440badce7006c269044aed9d9e223062cf8940e0440badce7006c269044aed9d9e223062cf8940e0origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#100601062626729BIOFORMATS-build #100100falsefalse1003683SUCCESS1791065284122https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/100/testintegration0f56ae9e3c5d57fb5ddbe7cb8cdffaca70e83a681791064887000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#146 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/146/) 2026-10-03 22:01:27 +00000f56ae9e3c5d57fb5ddbe7cb8cdffaca70e83a68merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit440badce7006c269044aed9d9e223062cf8940e01791065216000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..cf21ea57 Previously merged: - PR 487 pwalczysko 'Gatan2' - PR 486 pwalczysko 'Exclude gatan urls: 429 too many redirects' - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..9d5baf57d7 Previously merged: - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4487 sbesson 'TiffParser: log failed endian check at DEBUG level' - PR 4486 melissalinkert 'Upgrade check cleanup' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#146 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/146/) 2026-10-03 22:06:56 +0000440badce7006c269044aed9d9e223062cf8940e0merge master -Dorg -Ssuccess-onlyeditome-poieditbio-formats-documentationeditbio-formats-exampleseditbioformatsedit.gitmoduleseditome-common-javaeditome-modeleditome-mdbtoolseditome-metakiteditome-jaieditome-codecseditZarrReadereditome-stubsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop100https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/100/Started by upstream project "Trigger" build number 11Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue1226ce8f736a38261ebb77afbbb119519014af811226ce8f736a38261ebb77afbbb119519014af811origin/merge_ci226ce8f736a38261ebb77afbbb119519014af811226ce8f736a38261ebb77afbbb119519014af811origin/merge_ci226ce8f736a38261ebb77afbbb119519014af811226ce8f736a38261ebb77afbbb119519014af811origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#1308458626729BIOFORMATS-build #11falsefalse116FAILURE1783343847945https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/1/testintegrationgit1https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/1/Started by upstream project "Trigger" build number 118118Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue100440badce7006c269044aed9d9e223062cf8940e0440badce7006c269044aed9d9e223062cf8940e0origin/merge_ci440badce7006c269044aed9d9e223062cf8940e0440badce7006c269044aed9d9e223062cf8940e0origin/merge_ci440badce7006c269044aed9d9e223062cf8940e0440badce7006c269044aed9d9e223062cf8940e0origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#100601062626729BIOFORMATS-build #100100falsefalse1003683SUCCESS1791065284122https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/100/testintegration0f56ae9e3c5d57fb5ddbe7cb8cdffaca70e83a681791064887000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#146 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/146/) 2026-10-03 22:01:27 +00000f56ae9e3c5d57fb5ddbe7cb8cdffaca70e83a68merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit440badce7006c269044aed9d9e223062cf8940e01791065216000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..cf21ea57 Previously merged: - PR 487 pwalczysko 'Gatan2' - PR 486 pwalczysko 'Exclude gatan urls: 429 too many redirects' - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..9d5baf57d7 Previously merged: - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4487 sbesson 'TiffParser: log failed endian check at DEBUG level' - PR 4486 melissalinkert 'Upgrade check cleanup' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#146 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/146/) 2026-10-03 22:06:56 +0000440badce7006c269044aed9d9e223062cf8940e0merge master -Dorg -Ssuccess-onlyeditome-poieditbio-formats-documentationeditbio-formats-exampleseditbioformatsedit.gitmoduleseditome-common-javaeditome-modeleditome-mdbtoolseditome-metakiteditome-jaieditome-codecseditZarrReadereditome-stubsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop100https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/100/Started by upstream project "Trigger" build number 118118Triggerjob/Trigger/SKIP_DOCS_VALIDATIONtrue100440badce7006c269044aed9d9e223062cf8940e0440badce7006c269044aed9d9e223062cf8940e0origin/merge_ci440badce7006c269044aed9d9e223062cf8940e0440badce7006c269044aed9d9e223062cf8940e0origin/merge_ci440badce7006c269044aed9d9e223062cf8940e0440badce7006c269044aed9d9e223062cf8940e0origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#100601062626729BIOFORMATS-build #100100falsefalse1003683SUCCESS1791065284122https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/100/testintegration0f56ae9e3c5d57fb5ddbe7cb8cdffaca70e83a681791064887000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#146 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/146/) 2026-10-03 22:01:27 +00000f56ae9e3c5d57fb5ddbe7cb8cdffaca70e83a68merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit440badce7006c269044aed9d9e223062cf8940e01791065216000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Repository: ome/ZarrReader Updating 31d6d95..5f3faa4 Previously merged: - PR 111 Tom-TBT 'Fixed typo in README env var name to set' Repository: ome/bio-formats-documentation Updating db99c10d..cf21ea57 Previously merged: - PR 487 pwalczysko 'Gatan2' - PR 486 pwalczysko 'Exclude gatan urls: 429 too many redirects' - PR 485 sbesson 'cellSens/VSI: add OlyVIA as the reference software' - PR 484 pwalczysko 'Ignore loc.gov because of captcha' - PR 483 melissalinkert 'Add section on deprecated API' - PR 482 melissalinkert 'Minor issue tracker cleanup and clarify writing open formats' - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' - PR 476 melissalinkert 'Update logback to 1.5.37' - PR 477 melissalinkert 'Replace Olympus SIS link' - PR 471 dominikl 'Replace faqs.org links' - PR 474 dominikl 'exclude unidata' - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' - PR 472 dominikl 'ignore nih.gov' - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 469 sbesson 'Update Unidata releases URL' - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' - PR 465 pwalczysko 'Ignore umassmed.edu, 403' - PR 463 pwalczysko 'Ignore zenodo 403' - PR 461 melissalinkert 'Release notes for 8.5.0' - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' - PR 458 pwalczysko 'Konica olympus' - PR 455 melissalinkert 'Add TFCYTO page' - PR 454 melissalinkert 'Release notes for 8.4.0' - PR 453 pwalczysko 'Fix links' - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' - PR 450 melissalinkert 'Update a couple of outdated lines in about page' - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' - PR 445 melissalinkert 'Update ome-common to 6.1.1' - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 442 will-moore 'Link to Receipt of Sample Data' - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' - PR 441 melissalinkert 'Update external readers page based upon feedback' - PR 439 melissalinkert 'Start describing external reader usage' - PR 438 will-moore 'Fix netcdf-java links' - PR 437 pwalczysko 'Nis elements and cibc-datasets' - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' - PR 434 sbesson 'Add format page for Zeiss XRM format' - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' - PR 431 pwalczysko 'Fix limited javadoc syntax' - PR 430 pwalczysko 'Fix sourceforge' - PR 426 jburel 'Update EMAN2 URL' - PR 427 jburel 'Checking linkcheck config' - PR 422 melissalinkert 'Add page for JDCE' - PR 425 melissalinkert 'Release notes for 8.2.0' - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' - PR 418 sbesson 'Update MATLAB documentation for colormap return value' - PR 421 dominikl 'Exclude merckmillipore.com from link check' Merged PRs: - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' Repository: ome/bio-formats-examples Updating 3aa7013..669e8f3 Previously merged: - PR 139 melissalinkert 'Fix markers for tile conversion example' - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' - PR 136 melissalinkert 'Add precompressed tile writing example' - PR 137 melissalinkert 'Fix output path for in-memory writing test' - PR 135 melissalinkert 'Bump logback version to 1.3.16' - PR 134 sbesson 'POM: cleanup outdated metadata' Repository: openmicroscopy/bioformats Excluded PRs: - PR 4476 Darlokt 'Keep Windows volume identity in memo cache paths' (user: Darlokt) - PR 4470 PEEKPerformer 'OIR: resolve pixel block paths through the Location mapping' (user: PEEKPerformer) - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) Updating 3f70394503..9d5baf57d7 Previously merged: - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' - PR 4487 sbesson 'TiffParser: log failed endian check at DEBUG level' - PR 4486 melissalinkert 'Upgrade check cleanup' - PR 4479 melissalinkert 'Physical sizes for subresolutions' - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' - PR 4483 melissalinkert 'Minor updates to make it easier to extend `OMETiffReader`' - PR 4481 melissalinkert 'CV7000/8000: use `Target` as channel name if unique' - PR 4484 melissalinkert 'Exporter plugin: sanity check bits per pixel fields' - PR 4482 melissalinkert 'Remove unused and unpackaged `TJExample` and `TJUnitTest`' - PR 4478 melissalinkert 'TIFF: fix channel unpacking when supplied buffer is too large' - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' - PR 4445 melissalinkert '.vsi fill color fixes' - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' - PR 4452 melissalinkert 'Update logback to 1.5.37' - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' - PR 4438 melissalinkert 'Remove unnecessary negative checks' - PR 4436 melissalinkert 'xmlvalid cleanup' - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' - PR 4406 sbesson 'Fix Javadoc warnings' - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' - PR 4392 melissalinkert 'A few more ND2 dimension fixes' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' - PR 4388 melissalinkert 'Update to CodeQL v4' - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' - PR 4384 melissalinkert 'Update ome-common to 6.1.1' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' - PR 4374 melissalinkert 'CellH5: reduce memory usage' - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' - PR 4360 melissalinkert 'Fix several OIR issues' - PR 4365 melissalinkert 'Fix array sizes in Octave' - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' - PR 4361 melissalinkert 'Remove unused detector linking logic' - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' - PR 4353 melissalinkert 'Fix tag encoding for LEO files' - PR 4348 sbesson 'FakeReader: link instrument to all images' - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' - PR 4307 jburel 'Build report' - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' - PR 4338 sbesson 'org.openmicroscopy component updates' - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' - PR 4327 melissalinkert 'Check modulo values in repository tests' - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' - PR 4284 ptahmose 'fix for garbled images with CZIs' - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' - PR 4303 melissalinkert 'Fix Unidata repository URLs' Merged PRs: - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' - PR 4485 melissalinkert 'Operetta: normalize file separators' Repository: ome/ome-codecs Updating fab1a01..61a7334 Previously merged: - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-common-java Updating 2cb0b7b..a704a2a Previously merged: - PR 108 dominikl 'Remove S3 handling' - PR 117 melissalinkert 'Update logback to 1.5.37' - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' - PR 112 melissalinkert 'Standardize XML parsing' - PR 111 sbesson 'XMLTools: use try-with-resources statement' - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' - PR 107 sbesson 'Add GitHub release creation to Maven workflow' - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' - PR 99 melissalinkert 'Fix type of skipped bytes counter' - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' Repository: ome/ome-jai Updating e70c2ab..029d825 Previously merged: - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 8 sbesson 'Update publication build system to use Central Portal ' - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' Repository: ome/ome-mdbtools Updating 9193930..5224181 Previously merged: - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..b953d0b Previously merged: - PR 34 melissalinkert 'Update logback to 1.5.37' - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 30 melissalinkert 'Update ome-common to 6.1.1' - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' - PR 27 sbesson 'Update publication build system to use Central Portal' Repository: ome/ome-model Updating 3d70a1f9..57972947 Previously merged: - PR 236 sbesson 'Cap ruff version to 0.15.x and bump GitHub Action to run on Node.js 24' - PR 232 melissalinkert 'Update logback to 1.5.37' - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' - PR 225 melissalinkert 'Update ome-common to 6.1.1' - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' - PR 224 sbesson 'Add release step to GitHub Maven workflow' - PR 222 sbesson 'Update publication build system to use Central Portal' - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' Merged PRs: - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' Repository: ome/ome-poi Updating da3a5f3..f179bf4 Previously merged: - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-stubs Updating 1559997..5a2fdd0 Previously merged: - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' - PR 12 sbesson 'Update publication build system to use Central Portal' Merged PRs: - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' Generated by BIOFORMATS-push#146 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/146/) 2026-10-03 22:06:56 +0000440badce7006c269044aed9d9e223062cf8940e0merge master -Dorg 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