https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/BIOFORMATS-imageBIOFORMATS-imageBIOFORMATS-imageBIOFORMATS-imagehttps://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/trueStarted by upstream project "Trigger" build number 5050Triggerjob/Trigger/4336e3beba007496f2eca3578ef3e9b1410864afc036e3beba007496f2eca3578ef3e9b1410864afc0origin/merge_ci36e3beba007496f2eca3578ef3e9b1410864afc036e3beba007496f2eca3578ef3e9b1410864afc0origin/merge_ci36e3beba007496f2eca3578ef3e9b1410864afc036e3beba007496f2eca3578ef3e9b1410864afc0origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#43681729653283BIOFORMATS-image #4343falsefalse431218SUCCESS1786234533516https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/43/dockera1a6e99bc8e4275c759c4b8f58d70ab9364df5271786233681000https://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-onlyeditbio-formats-documentationeditome-codecseditome-common-javaeditbio-formats-exampleseditZarrReadereditome-mdbtoolseditome-modeleditome-stubsedit.gitmoduleseditbioformatseditome-jaieditome-poieditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 4949Triggerjob/Trigger/4257e62c88a950f1a0571e0ae20b8494e01d0cd5c657e62c88a950f1a0571e0ae20b8494e01d0cd5c6origin/merge_ci57e62c88a950f1a0571e0ae20b8494e01d0cd5c657e62c88a950f1a0571e0ae20b8494e01d0cd5c6origin/merge_ci57e62c88a950f1a0571e0ae20b8494e01d0cd5c657e62c88a950f1a0571e0ae20b8494e01d0cd5c6origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#42669440653283BIOFORMATS-image #4242falsefalse421174SUCCESS1786148121600https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/42/docker48e148e9782defa84bb2d6d6d339d45f56080a2c1786147265000https://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-documentationome-modelZarrReaderome-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-onlyedit.gitmoduleseditome-codecseditbioformatseditome-jaieditome-mdbtoolseditome-poieditome-metakiteditbio-formats-documentationeditbio-formats-exampleseditome-common-javaeditome-stubseditome-modeleditZarrReadergithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 4848Triggerjob/Trigger/416e71bbcbea234823b8a053c1d967f8000d90ccc06e71bbcbea234823b8a053c1d967f8000d90ccc0origin/merge_ci6e71bbcbea234823b8a053c1d967f8000d90ccc06e71bbcbea234823b8a053c1d967f8000d90ccc0origin/merge_ci6e71bbcbea234823b8a053c1d967f8000d90ccc06e71bbcbea234823b8a053c1d967f8000d90ccc0origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#41608679653283BIOFORMATS-image #4141falsefalse411130SUCCESS1786103655545https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/41/dockerc912ec448bf278f4ef2a178a1484cc93ad59113b1786102813000https://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-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-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-mdbtoolseditome-poieditome-jaieditome-stubseditome-codecseditbio-formats-exampleseditome-common-javaeditbioformatseditome-modeledit.gitmoduleseditbio-formats-documentationeditZarrReadergithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 4747Triggerjob/Trigger/405b5f3a239078cc812d8cdb6004912d43f65ee8745b5f3a239078cc812d8cdb6004912d43f65ee874origin/merge_ci5b5f3a239078cc812d8cdb6004912d43f65ee8745b5f3a239078cc812d8cdb6004912d43f65ee874origin/merge_ci5b5f3a239078cc812d8cdb6004912d43f65ee8745b5f3a239078cc812d8cdb6004912d43f65ee874origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#40613020653283BIOFORMATS-image #4040falsefalse401083SUCCESS1786061748756https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/40/docker654f280a08a90404266fafaefd7f4ee083a2d0171786060872000https://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-java.gitmodulesbioformatsome-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-mdbtoolseditome-metakiteditZarrReaderedit.gitmoduleseditome-modeleditbioformatseditome-stubseditome-jaieditome-codecseditbio-formats-exampleseditome-poieditbio-formats-documentationeditome-common-javagithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 4646Triggerjob/Trigger/39839397a0c63f39867367875f82abd423205288a7839397a0c63f39867367875f82abd423205288a7origin/merge_ci839397a0c63f39867367875f82abd423205288a7839397a0c63f39867367875f82abd423205288a7origin/merge_ci839397a0c63f39867367875f82abd423205288a7839397a0c63f39867367875f82abd423205288a7origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#39641776653283BIOFORMATS-image #3939falsefalse391039SUCCESS1785975321840https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/39/dockerd996dc9275dc8eac16b28ffb88afec21fe5afa6d1785974478000https://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-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-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-onlyeditome-metakiteditome-common-javaedit.gitmoduleseditome-jaieditome-poieditome-codecseditbio-formats-exampleseditome-stubseditbio-formats-documentationeditbioformatseditome-modeleditZarrReadereditome-mdbtoolsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 4545Triggerjob/Trigger/38998240446b12c9685f4d24c58a63b3396e3e6e5d998240446b12c9685f4d24c58a63b3396e3e6e5dorigin/merge_ci998240446b12c9685f4d24c58a63b3396e3e6e5d998240446b12c9685f4d24c58a63b3396e3e6e5dorigin/merge_ci998240446b12c9685f4d24c58a63b3396e3e6e5d998240446b12c9685f4d24c58a63b3396e3e6e5dorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#38617337653283BIOFORMATS-image #3838falsefalse38995SUCCESS1785889059830https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/38/dockergitStarted by upstream project "Trigger" build number 4444Triggerjob/Trigger/371390b2a6d780dfcbd8127b6da02ad5344316fdc31390b2a6d780dfcbd8127b6da02ad5344316fdc3origin/merge_ci1390b2a6d780dfcbd8127b6da02ad5344316fdc31390b2a6d780dfcbd8127b6da02ad5344316fdc3origin/merge_ci1390b2a6d780dfcbd8127b6da02ad5344316fdc31390b2a6d780dfcbd8127b6da02ad5344316fdc3origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#37610678653283BIOFORMATS-image #3737falsefalse37946SUCCESS1785802492174https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/37/docker30170eb8a1f2330d75242aa02f3b0834990dd2981785801674000https://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-stubseditome-metakiteditome-jaieditome-poieditome-modeledit.gitmoduleseditome-common-javaeditome-mdbtoolseditbio-formats-documentationeditbio-formats-exampleseditbioformatseditZarrReadereditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 4343Triggerjob/Trigger/36f89cf943b5380ec5ef5a973079d3fd88c6b2bb7ff89cf943b5380ec5ef5a973079d3fd88c6b2bb7forigin/merge_cif89cf943b5380ec5ef5a973079d3fd88c6b2bb7ff89cf943b5380ec5ef5a973079d3fd88c6b2bb7forigin/merge_cif89cf943b5380ec5ef5a973079d3fd88c6b2bb7ff89cf943b5380ec5ef5a973079d3fd88c6b2bb7forigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#36658208653283BIOFORMATS-image #3636falsefalse36895SUCCESS1785716090157https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/36/docker29812db8b4cf9b092769d6edce816cb222927b591785715278000https://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-documentationome-modelZarrReaderome-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-onlyeditome-codecseditome-stubseditome-modeleditbio-formats-exampleseditZarrReadereditome-common-javaeditbioformatseditome-jaieditbio-formats-documentationeditome-mdbtoolseditome-poiedit.gitmoduleseditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 4242Triggerjob/Trigger/351e41bde2e17e3b5a4306a545656b51693a0f60831e41bde2e17e3b5a4306a545656b51693a0f6083origin/merge_ci1e41bde2e17e3b5a4306a545656b51693a0f60831e41bde2e17e3b5a4306a545656b51693a0f6083origin/merge_ci1e41bde2e17e3b5a4306a545656b51693a0f60831e41bde2e17e3b5a4306a545656b51693a0f6083origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#35702309653283BIOFORMATS-image #3535falsefalse35851SUCCESS1785658021077https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/35/docker8b20f4859c90ece02f9a31cb2a3e3f83007b07e61785657175000https://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-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-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-documentationeditome-codecseditome-jaieditome-metakiteditome-stubseditbio-formats-exampleseditome-poiedit.gitmoduleseditbioformatseditome-modeleditZarrReadereditome-common-javaeditome-mdbtoolsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 4141Triggerjob/Trigger/34f1ad5633c9a08eb2b2713b2ff98fe8e8960ef171f1ad5633c9a08eb2b2713b2ff98fe8e8960ef171origin/merge_cif1ad5633c9a08eb2b2713b2ff98fe8e8960ef171f1ad5633c9a08eb2b2713b2ff98fe8e8960ef171origin/merge_cif1ad5633c9a08eb2b2713b2ff98fe8e8960ef171f1ad5633c9a08eb2b2713b2ff98fe8e8960ef171origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#34641432653283BIOFORMATS-image #3434falsefalse34807SUCCESS1785629696671https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/34/docker0ee3db438f0c2bace01731c9f07c43f04ff5ddce1785628877000https://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-java.gitmodulesbioformatsome-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-onlyeditome-modeleditbio-formats-exampleseditome-codecseditome-common-javaeditome-mdbtoolseditome-metakiteditZarrReadereditbio-formats-documentationedit.gitmoduleseditome-poieditome-jaieditbioformatseditome-stubsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 4040Triggerjob/Trigger/33cd2813e70c774c33746499242844b6b56872667ecd2813e70c774c33746499242844b6b56872667eorigin/merge_cicd2813e70c774c33746499242844b6b56872667ecd2813e70c774c33746499242844b6b56872667eorigin/merge_cicd2813e70c774c33746499242844b6b56872667ecd2813e70c774c33746499242844b6b56872667eorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#33670525653283BIOFORMATS-image #3333falsefalse33762SUCCESS1785581341558https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/33/dockergitStarted by upstream project "Trigger" build number 3838Triggerjob/Trigger/32a2235e57dc7e95570f74d164bd51419369820e0da2235e57dc7e95570f74d164bd51419369820e0dorigin/merge_cia2235e57dc7e95570f74d164bd51419369820e0da2235e57dc7e95570f74d164bd51419369820e0dorigin/merge_cia2235e57dc7e95570f74d164bd51419369820e0da2235e57dc7e95570f74d164bd51419369820e0dorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#32648282653283BIOFORMATS-image #3232falsefalse32709SUCCESS1785456909919https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/32/docker48952f017a407a71448d521a0055c66a194c7eae1785456081000https://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-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-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-onlyedit.gitmoduleseditome-common-javaeditome-mdbtoolseditome-modeleditbio-formats-exampleseditome-poieditZarrReadereditome-codecseditome-metakiteditbio-formats-documentationeditome-stubseditbioformatseditome-jaigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 3737Triggerjob/Trigger/31789b9856c6e27bb3eec0f4a72ab0a21ed37a28c5789b9856c6e27bb3eec0f4a72ab0a21ed37a28c5origin/merge_ci789b9856c6e27bb3eec0f4a72ab0a21ed37a28c5789b9856c6e27bb3eec0f4a72ab0a21ed37a28c5origin/merge_ci789b9856c6e27bb3eec0f4a72ab0a21ed37a28c5789b9856c6e27bb3eec0f4a72ab0a21ed37a28c5origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#31638852653283BIOFORMATS-image #3131falsefalse31665SUCCESS1785370507943https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/31/docker5994452b90599f98bdd70dbeb3d18dcd5bed54b61785369691000https://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-documentationome-modelZarrReaderome-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-mdbtoolseditome-common-javaeditome-metakiteditome-modeleditbio-formats-exampleseditbio-formats-documentationeditome-poieditZarrReaderedit.gitmoduleseditome-jaieditbioformatseditome-stubseditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 3636Triggerjob/Trigger/30f34448d4eb73ee1f4bbfc8d1d3d2c213960a7ab5f34448d4eb73ee1f4bbfc8d1d3d2c213960a7ab5origin/merge_cif34448d4eb73ee1f4bbfc8d1d3d2c213960a7ab5f34448d4eb73ee1f4bbfc8d1d3d2c213960a7ab5origin/merge_cif34448d4eb73ee1f4bbfc8d1d3d2c213960a7ab5f34448d4eb73ee1f4bbfc8d1d3d2c213960a7ab5origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#30614718653283BIOFORMATS-image #3030falsefalse30615SUCCESS1785325981804https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/30/dockergitStarted by upstream project "Trigger" build number 3434Triggerjob/Trigger/29831235ddc989f534c60e87bed66b35704c84aec5831235ddc989f534c60e87bed66b35704c84aec5origin/merge_ci831235ddc989f534c60e87bed66b35704c84aec5831235ddc989f534c60e87bed66b35704c84aec5origin/merge_ci831235ddc989f534c60e87bed66b35704c84aec5831235ddc989f534c60e87bed66b35704c84aec5origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#29794183653283BIOFORMATS-image #2929falsefalse29548SUCCESS1785244653723https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/29/dockergitStarted by upstream project "Trigger" build number 3131Triggerjob/Trigger/28265f2da39559c56213e0a9e0164f41736e3017ed265f2da39559c56213e0a9e0164f41736e3017edorigin/merge_ci265f2da39559c56213e0a9e0164f41736e3017ed265f2da39559c56213e0a9e0164f41736e3017edorigin/merge_ci265f2da39559c56213e0a9e0164f41736e3017ed265f2da39559c56213e0a9e0164f41736e3017edorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#28606027653283BIOFORMATS-image #2828falsefalse28497SUCCESS1785111312922https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/28/dockerfc4a4c9014186586000e5b7d9a13dd96903c1ab21785110476000https://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-java.gitmodulesbioformatsome-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-mdbtoolseditome-modeledit.gitmoduleseditZarrReadereditbio-formats-exampleseditome-codecseditome-poieditbio-formats-documentationeditbioformatseditome-stubseditome-common-javaeditome-metakiteditome-jaigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 3030Triggerjob/Trigger/27906c4d72b69e1aaad611a8ab2f40668ba2ad04aa906c4d72b69e1aaad611a8ab2f40668ba2ad04aaorigin/merge_ci906c4d72b69e1aaad611a8ab2f40668ba2ad04aa906c4d72b69e1aaad611a8ab2f40668ba2ad04aaorigin/merge_ci906c4d72b69e1aaad611a8ab2f40668ba2ad04aa906c4d72b69e1aaad611a8ab2f40668ba2ad04aaorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#27589997653283BIOFORMATS-image #2727falsefalse27453SUCCESS1785024935819https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/27/dockercd83788b4ea63dd41f9958403dadb38042c3e3f41785024078000https://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-java.gitmodulesbioformatsome-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-onlyeditome-mdbtoolseditbio-formats-exampleseditome-codecseditome-common-javaeditome-metakiteditome-stubseditbio-formats-documentationeditZarrReadereditome-jaiedit.gitmoduleseditome-modeleditome-poieditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 2929Triggerjob/Trigger/265cb19f1d7e0ce1506b52140558187eb39792c6a45cb19f1d7e0ce1506b52140558187eb39792c6a4origin/merge_ci5cb19f1d7e0ce1506b52140558187eb39792c6a45cb19f1d7e0ce1506b52140558187eb39792c6a4origin/merge_ci5cb19f1d7e0ce1506b52140558187eb39792c6a45cb19f1d7e0ce1506b52140558187eb39792c6a4origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#26631609653283BIOFORMATS-image #2626falsefalse26409SUCCESS1784938528802https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/26/dockere3d284428f1d2ba5fcea32d48100ce1dd6fb31ad1784937675000https://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-common-javaedit.gitmoduleseditome-jaieditome-modeleditome-poieditbio-formats-documentationeditbio-formats-exampleseditome-codecseditZarrReadereditome-mdbtoolseditbioformatseditome-metakiteditome-stubsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 2828Triggerjob/Trigger/2574f853514947a38d7eb7cf6481791ce4596c713374f853514947a38d7eb7cf6481791ce4596c7133origin/merge_ci74f853514947a38d7eb7cf6481791ce4596c713374f853514947a38d7eb7cf6481791ce4596c7133origin/merge_ci74f853514947a38d7eb7cf6481791ce4596c713374f853514947a38d7eb7cf6481791ce4596c7133origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#25600397653283BIOFORMATS-image #2525falsefalse25365SUCCESS1784852156893https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/25/docker1a72d49caf324d214716460958ef393b69c04d301784851279000https://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-onlyeditome-mdbtoolseditome-jaieditome-modeleditome-metakiteditbioformatseditbio-formats-documentationeditome-codecseditZarrReadereditome-poieditome-stubseditbio-formats-examplesedit.gitmoduleseditome-common-javagithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 2727Triggerjob/Trigger/248ec86f061ec5b1affb8f798bc4b9c088b33bcde88ec86f061ec5b1affb8f798bc4b9c088b33bcde8origin/merge_ci8ec86f061ec5b1affb8f798bc4b9c088b33bcde88ec86f061ec5b1affb8f798bc4b9c088b33bcde8origin/merge_ci8ec86f061ec5b1affb8f798bc4b9c088b33bcde88ec86f061ec5b1affb8f798bc4b9c088b33bcde8origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#24585484653283BIOFORMATS-image #2424falsefalse24321SUCCESS1784765704933https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/24/docker245f594296856b17191ba886ad5aedfad34036b01784764872000https://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-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-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-onlyeditbioformatseditbio-formats-documentationeditome-modeleditome-mdbtoolseditome-metakitedit.gitmoduleseditbio-formats-exampleseditome-stubseditome-codecseditome-poieditome-common-javaeditome-jaieditZarrReadergithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 2626Triggerjob/Trigger/23e8cea1dba0ab458cbc5e918a63f9069c9c9cc65ee8cea1dba0ab458cbc5e918a63f9069c9c9cc65eorigin/merge_cie8cea1dba0ab458cbc5e918a63f9069c9c9cc65ee8cea1dba0ab458cbc5e918a63f9069c9c9cc65eorigin/merge_cie8cea1dba0ab458cbc5e918a63f9069c9c9cc65ee8cea1dba0ab458cbc5e918a63f9069c9c9cc65eorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#23610294653283BIOFORMATS-image #2323falsefalse23277SUCCESS1784718238956https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/23/dockergitStarted by upstream project "Trigger" build number 2424Triggerjob/Trigger/229a04ac44306530cbea4eed8ce96bc73e526aaadc9a04ac44306530cbea4eed8ce96bc73e526aaadcorigin/merge_ci9a04ac44306530cbea4eed8ce96bc73e526aaadc9a04ac44306530cbea4eed8ce96bc73e526aaadcorigin/merge_ci9a04ac44306530cbea4eed8ce96bc73e526aaadc9a04ac44306530cbea4eed8ce96bc73e526aaadcorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#22601984653283BIOFORMATS-image #2222falsefalse22211SUCCESS1784592925363https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/22/docker4a2eed50d51466b5cc6c9d1732a48ca5791bcc5d1784592084000https://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-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-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-onlyeditome-metakitedit.gitmoduleseditbio-formats-documentationeditome-common-javaeditome-stubseditbioformatseditome-codecseditome-modeleditome-mdbtoolseditbio-formats-exampleseditZarrReadereditome-poieditome-jaigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 2323Triggerjob/Trigger/21d958d5f126d0779e3b072a3cff1e7e56b3645c28d958d5f126d0779e3b072a3cff1e7e56b3645c28origin/merge_cid958d5f126d0779e3b072a3cff1e7e56b3645c28d958d5f126d0779e3b072a3cff1e7e56b3645c28origin/merge_cid958d5f126d0779e3b072a3cff1e7e56b3645c28d958d5f126d0779e3b072a3cff1e7e56b3645c28origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#21629027653283BIOFORMATS-image #2121falsefalse21167SUCCESS1784537044131https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/21/dockereb948dc502409d8e842d57505b4fbdd40322a6951784536164000https://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-documentationome-modelZarrReaderome-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-onlyeditbioformatseditome-stubseditbio-formats-documentationeditome-modeleditbio-formats-exampleseditome-codecseditome-mdbtoolseditome-common-javaeditZarrReadereditome-jaieditome-metakitedit.gitmoduleseditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 2121Triggerjob/Trigger/202fdfce74df4b02f988fc2165a5c88573e06131892fdfce74df4b02f988fc2165a5c88573e0613189origin/merge_ci2fdfce74df4b02f988fc2165a5c88573e06131892fdfce74df4b02f988fc2165a5c88573e0613189origin/merge_ci2fdfce74df4b02f988fc2165a5c88573e06131892fdfce74df4b02f988fc2165a5c88573e0613189origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#20671510653283BIOFORMATS-image #2020falsefalse20119SUCCESS1784420276556https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/20/dockere3b37dde5d711a2b94ba9734bbaa6a3d61a840681784419279000https://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-documentationZarrReaderome-modelome-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-codecseditbio-formats-exampleseditome-stubsedit.gitmoduleseditome-jaieditbioformatseditbio-formats-documentationeditome-common-javaeditome-metakiteditZarrReadereditome-poieditome-mdbtoolseditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 2020Triggerjob/Trigger/19cecc40b71b35b31a9b7bee29e4b2b84dfa0d6aafcecc40b71b35b31a9b7bee29e4b2b84dfa0d6aaforigin/merge_cicecc40b71b35b31a9b7bee29e4b2b84dfa0d6aafcecc40b71b35b31a9b7bee29e4b2b84dfa0d6aaforigin/merge_cicecc40b71b35b31a9b7bee29e4b2b84dfa0d6aafcecc40b71b35b31a9b7bee29e4b2b84dfa0d6aaforigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#19607865653283BIOFORMATS-image #1919falsefalse1975SUCCESS1784333764610https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/19/docker8d8dab5b0e2820950c2d0849cd2d0ad10d1de6cd1784332876000https://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-javabioformats.gitmodulesome-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-onlyeditbioformatseditome-mdbtoolsedit.gitmoduleseditbio-formats-documentationeditome-stubseditbio-formats-exampleseditome-codecseditome-modeleditome-poieditome-jaieditZarrReadereditome-common-javaeditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 1818Triggerjob/Trigger/183110d7046bfcc18a1e1487bc195dbd1d95598bec3110d7046bfcc18a1e1487bc195dbd1d95598becorigin/merge_ci3110d7046bfcc18a1e1487bc195dbd1d95598bec3110d7046bfcc18a1e1487bc195dbd1d95598becorigin/merge_ci3110d7046bfcc18a1e1487bc195dbd1d95598bec3110d7046bfcc18a1e1487bc195dbd1d95598becorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#18596992653283BIOFORMATS-image #1818falsefalse1825SUCCESS1784197979432https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/18/docker39a8cb6f6d695bfe6a1d2d3f412b7c3624ce75d11784197181000https://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-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-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-poiedit.gitmoduleseditbio-formats-documentationeditbio-formats-exampleseditbioformatseditome-codecseditome-metakiteditome-modeleditome-stubseditome-common-javaeditome-mdbtoolseditZarrReadereditome-jaigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 1717Triggerjob/Trigger/178718ccf5c033534a8ba51cca7f3c84bd14abd7008718ccf5c033534a8ba51cca7f3c84bd14abd700origin/merge_ci8718ccf5c033534a8ba51cca7f3c84bd14abd7008718ccf5c033534a8ba51cca7f3c84bd14abd700origin/merge_ci8718ccf5c033534a8ba51cca7f3c84bd14abd7008718ccf5c033534a8ba51cca7f3c84bd14abd700origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#17600184653283BIOFORMATS-image #1717falsefalse176SUCCESS1784193039284https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/17/dockergitStarted by upstream project "Trigger" build number 1616Triggerjob/Trigger/166dc2aea500a71d7c84e35b2bf5cb3841b573cff76dc2aea500a71d7c84e35b2bf5cb3841b573cff7origin/merge_ci6dc2aea500a71d7c84e35b2bf5cb3841b573cff76dc2aea500a71d7c84e35b2bf5cb3841b573cff7origin/merge_ci6dc2aea500a71d7c84e35b2bf5cb3841b573cff76dc2aea500a71d7c84e35b2bf5cb3841b573cff7origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#16649874653283BIOFORMATS-image #1616falsefalse16524SUCCESS1784161049851https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/16/dockergitStarted by upstream project "Trigger" build number 1414Triggerjob/Trigger/15663dd3fe9892cd073d6493c94e0ea9971e74c206663dd3fe9892cd073d6493c94e0ea9971e74c206origin/merge_ci663dd3fe9892cd073d6493c94e0ea9971e74c206663dd3fe9892cd073d6493c94e0ea9971e74c206origin/merge_ci663dd3fe9892cd073d6493c94e0ea9971e74c206663dd3fe9892cd073d6493c94e0ea9971e74c206origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#15624295653283BIOFORMATS-image #1515falsefalse15474SUCCESS1784018804788https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/15/dockergithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 1313Triggerjob/Trigger/14e64b26a26ae6fffd9692b80136095535e7521cbce64b26a26ae6fffd9692b80136095535e7521cbcorigin/merge_cie64b26a26ae6fffd9692b80136095535e7521cbce64b26a26ae6fffd9692b80136095535e7521cbcorigin/merge_cie64b26a26ae6fffd9692b80136095535e7521cbce64b26a26ae6fffd9692b80136095535e7521cbcorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#14558996653283BIOFORMATS-image #1414falsefalse14468FAILURE1783988093108https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/14/docker6e3e8df3ee1e8d8654d09f47bba73d7285efeaff1783987270000https://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-javabioformats.gitmodulesome-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-onlyeditbio-formats-exampleseditbioformatseditome-mdbtoolseditome-stubseditZarrReadereditome-jaieditome-poieditbio-formats-documentationeditome-codecsedit.gitmoduleseditome-metakiteditome-modeleditome-common-javagithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 1212Triggerjob/Trigger/13a8985293e6b42f17332a5f1cf2ddf7987260ac4da8985293e6b42f17332a5f1cf2ddf7987260ac4dorigin/merge_cia8985293e6b42f17332a5f1cf2ddf7987260ac4da8985293e6b42f17332a5f1cf2ddf7987260ac4dorigin/merge_cia8985293e6b42f17332a5f1cf2ddf7987260ac4da8985293e6b42f17332a5f1cf2ddf7987260ac4dorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#13569804653283BIOFORMATS-image #1313falsefalse13422SUCCESS1783901686300https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/13/docker4a4b222130971c9687da36e5c11a4b30345a5cf81783900873000https://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-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-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-onlyeditbio-formats-exampleseditome-poieditome-jaieditome-common-javaeditZarrReadereditome-mdbtoolseditome-modeleditome-stubseditbioformatseditbio-formats-documentationeditome-codecsedit.gitmoduleseditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 1111Triggerjob/Trigger/12be7f9d9124d570338384ef5eceb42acfcc1396cfbe7f9d9124d570338384ef5eceb42acfcc1396cforigin/merge_cibe7f9d9124d570338384ef5eceb42acfcc1396cfbe7f9d9124d570338384ef5eceb42acfcc1396cforigin/merge_cibe7f9d9124d570338384ef5eceb42acfcc1396cfbe7f9d9124d570338384ef5eceb42acfcc1396cforigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#12590021653283BIOFORMATS-image #1212falsefalse12378SUCCESS1783815308736https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/12/docker7ff92fc4e84c580cab75615d4143ccc89c2c49121783814475000https://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-onlyeditZarrReadereditbioformatseditbio-formats-documentationeditome-poieditome-stubseditome-jaieditome-common-javaeditome-mdbtoolsedit.gitmoduleseditome-modeleditbio-formats-exampleseditome-codecseditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 1010Triggerjob/Trigger/11400fbbd0de84c710bc2bc10afeb7997e41d21fa5400fbbd0de84c710bc2bc10afeb7997e41d21fa5origin/merge_ci400fbbd0de84c710bc2bc10afeb7997e41d21fa5400fbbd0de84c710bc2bc10afeb7997e41d21fa5origin/merge_ci400fbbd0de84c710bc2bc10afeb7997e41d21fa5400fbbd0de84c710bc2bc10afeb7997e41d21fa5origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#11571768653283BIOFORMATS-image #1111falsefalse11334SUCCESS1783729041919https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/11/dockergitStarted by upstream project "Trigger" build number 99Triggerjob/Trigger/10a8646c8bea484b8eb14e0a5b4504bb8b9053fa0ca8646c8bea484b8eb14e0a5b4504bb8b9053fa0corigin/merge_cia8646c8bea484b8eb14e0a5b4504bb8b9053fa0ca8646c8bea484b8eb14e0a5b4504bb8b9053fa0corigin/merge_cia8646c8bea484b8eb14e0a5b4504bb8b9053fa0ca8646c8bea484b8eb14e0a5b4504bb8b9053fa0corigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#10628490653283BIOFORMATS-image #1010falsefalse10284SUCCESS1783642503197https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/10/dockerae6f43549dd3f3c11ef6fdab418645eb260d19ae1783641672000https://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-javabioformats.gitmodulesome-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-metakiteditome-poieditbio-formats-exampleseditome-stubseditome-jaieditome-modeleditbio-formats-documentationeditZarrReadereditbioformatsedit.gitmoduleseditome-codecseditome-mdbtoolseditome-common-javagithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 88Triggerjob/Trigger/9c80f2d1a1f3c39cf728392ab1cd90527663d5a3ec80f2d1a1f3c39cf728392ab1cd90527663d5a3eorigin/merge_cic80f2d1a1f3c39cf728392ab1cd90527663d5a3ec80f2d1a1f3c39cf728392ab1cd90527663d5a3eorigin/merge_cic80f2d1a1f3c39cf728392ab1cd90527663d5a3ec80f2d1a1f3c39cf728392ab1cd90527663d5a3eorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#9951388653283BIOFORMATS-image #99falsefalse9222SUCCESS1783589946966https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/9/docker4673acf2ca38e5953a4446623f917bdaa3124d0f1783589087000https://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-javabioformats.gitmodulesome-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-codecseditbioformatseditome-jaieditome-common-javaeditome-poieditbio-formats-exampleseditome-modeleditome-stubsedit.gitmoduleseditZarrReadereditbio-formats-documentationeditome-mdbtoolseditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by user devspacedevspacedevspace8fc9a8aea56d4059b7581bb36146d8738640e49aefc9a8aea56d4059b7581bb36146d8738640e49aeorigin/merge_cifc9a8aea56d4059b7581bb36146d8738640e49aefc9a8aea56d4059b7581bb36146d8738640e49aeorigin/merge_cifc9a8aea56d4059b7581bb36146d8738640e49aefc9a8aea56d4059b7581bb36146d8738640e49aeorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#8944851653283BIOFORMATS-image #88falsefalse8214SUCCESS1783586299382https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/8/dockergitStarted by user devspacedevspacedevspace7fc9a8aea56d4059b7581bb36146d8738640e49aefc9a8aea56d4059b7581bb36146d8738640e49aeorigin/merge_cifc9a8aea56d4059b7581bb36146d8738640e49aefc9a8aea56d4059b7581bb36146d8738640e49aeorigin/merge_cifc9a8aea56d4059b7581bb36146d8738640e49aefc9a8aea56d4059b7581bb36146d8738640e49aeorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#7773717653283BIOFORMATS-image #77falsefalse7213FAILURE1783578544605https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/7/dockergitStarted by upstream project "Trigger" build number 77Triggerjob/Trigger/6fc9a8aea56d4059b7581bb36146d8738640e49aefc9a8aea56d4059b7581bb36146d8738640e49aeorigin/merge_cifc9a8aea56d4059b7581bb36146d8738640e49aefc9a8aea56d4059b7581bb36146d8738640e49aeorigin/merge_cifc9a8aea56d4059b7581bb36146d8738640e49aefc9a8aea56d4059b7581bb36146d8738640e49aeorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#6853183653283BIOFORMATS-image #66falsefalse6212FAILURE1783556216221https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/6/dockergitStarted by upstream project "Trigger" build number 66Triggerjob/Trigger/58e4245c75acc2fc115746a792bb0663c4576cbca8e4245c75acc2fc115746a792bb0663c4576cbcaorigin/merge_ci8e4245c75acc2fc115746a792bb0663c4576cbca8e4245c75acc2fc115746a792bb0663c4576cbcaorigin/merge_ci8e4245c75acc2fc115746a792bb0663c4576cbca8e4245c75acc2fc115746a792bb0663c4576cbcaorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#5575966653283BIOFORMATS-image #55falsefalse5149SUCCESS1783469668725https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/5/docker6d15fe69cea02417b083e2813ac5eeaf492ce5611783468868000https://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-documentationZarrReaderome-modelome-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-onlyeditome-metakitedit.gitmoduleseditome-codecseditome-poieditZarrReadereditome-stubseditbioformatseditome-common-javaeditome-modeleditome-mdbtoolseditome-jaieditbio-formats-documentationeditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 55Triggerjob/Trigger/42f5cfd10cd114d16d1d59b29fab12c7118ee7d622f5cfd10cd114d16d1d59b29fab12c7118ee7d62origin/merge_ci2f5cfd10cd114d16d1d59b29fab12c7118ee7d622f5cfd10cd114d16d1d59b29fab12c7118ee7d62origin/merge_ci2f5cfd10cd114d16d1d59b29fab12c7118ee7d622f5cfd10cd114d16d1d59b29fab12c7118ee7d62origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#4612917653283BIOFORMATS-image #44falsefalse4101SUCCESS1783422322566https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/4/dockergitStarted by upstream project "Trigger" build number 44Triggerjob/Trigger/30fcb2408b754357e32d6ace4bebc43cced0ba35d0fcb2408b754357e32d6ace4bebc43cced0ba35dorigin/merge_ci0fcb2408b754357e32d6ace4bebc43cced0ba35d0fcb2408b754357e32d6ace4bebc43cced0ba35dorigin/merge_ci0fcb2408b754357e32d6ace4bebc43cced0ba35d0fcb2408b754357e32d6ace4bebc43cced0ba35dorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#3605519653283BIOFORMATS-image #33falsefalse377SUCCESS1783383393928https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/3/docker6399110079f05b183f7b9e5c0d34ed04b777f34f1783382456000https://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-onlyeditZarrReadereditome-stubseditbio-formats-exampleseditbio-formats-documentationeditome-mdbtoolsedit.gitmoduleseditome-metakiteditome-common-javaeditome-modeleditome-poieditome-jaieditbioformatseditome-codecsbioformatsome-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-metakiteditbio-formats-documentationeditome-codecseditome-modeleditome-poieditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 33Triggerjob/Trigger/2c71805ba73148598305093dca665435e660fac2ec71805ba73148598305093dca665435e660fac2eorigin/merge_cic71805ba73148598305093dca665435e660fac2ec71805ba73148598305093dca665435e660fac2eorigin/merge_cic71805ba73148598305093dca665435e660fac2ec71805ba73148598305093dca665435e660fac2eorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#2544037653283BIOFORMATS-image #22falsefalse240SUCCESS1783349203140https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/2/docker61a3b6acae43bcf26041b281a5c2b4d3612b08fd1783348368000https://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-stubseditome-metakiteditbio-formats-exampleseditZarrReadereditome-codecseditome-jaieditome-modeleditome-mdbtoolseditbio-formats-documentationeditome-poieditbioformatsedit.gitmoduleseditome-common-javabioformatsome-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 versionseditbioformatseditbio-formats-documentationeditome-codecseditome-metakiteditome-modeleditome-poieditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 22Triggerjob/Trigger/1f5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206f5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206origin/merge_cif5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206f5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206origin/merge_cif5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206f5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#1627488653283BIOFORMATS-image #11falsefalse123SUCCESS1783345388024https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/1/dockergitblueStarted by upstream project "Trigger" build number 22Triggerjob/Trigger/1f5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206f5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206origin/merge_cif5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206f5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206origin/merge_cif5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206f5303d2e5bf2bb636a2b62a9c06a85b7a0f5f206origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#1627488653283BIOFORMATS-image #11falsefalse123SUCCESS1783345388024https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/1/dockergitBuild stability: No recent builds failed.icon-health-80plushealth-80plus.png100falsefalseStarted by upstream project "Trigger" build number 5050Triggerjob/Trigger/4336e3beba007496f2eca3578ef3e9b1410864afc036e3beba007496f2eca3578ef3e9b1410864afc0origin/merge_ci36e3beba007496f2eca3578ef3e9b1410864afc036e3beba007496f2eca3578ef3e9b1410864afc0origin/merge_ci36e3beba007496f2eca3578ef3e9b1410864afc036e3beba007496f2eca3578ef3e9b1410864afc0origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#43681729653283BIOFORMATS-image #4343falsefalse431218SUCCESS1786234533516https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/43/dockera1a6e99bc8e4275c759c4b8f58d70ab9364df5271786233681000https://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-onlyeditbio-formats-documentationeditome-codecseditome-common-javaeditbio-formats-exampleseditZarrReadereditome-mdbtoolseditome-modeleditome-stubsedit.gitmoduleseditbioformatseditome-jaieditome-poieditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 5050Triggerjob/Trigger/4336e3beba007496f2eca3578ef3e9b1410864afc036e3beba007496f2eca3578ef3e9b1410864afc0origin/merge_ci36e3beba007496f2eca3578ef3e9b1410864afc036e3beba007496f2eca3578ef3e9b1410864afc0origin/merge_ci36e3beba007496f2eca3578ef3e9b1410864afc036e3beba007496f2eca3578ef3e9b1410864afc0origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#43681729653283BIOFORMATS-image #4343falsefalse431218SUCCESS1786234533516https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/43/dockera1a6e99bc8e4275c759c4b8f58d70ab9364df5271786233681000https://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-onlyeditbio-formats-documentationeditome-codecseditome-common-javaeditbio-formats-exampleseditZarrReadereditome-mdbtoolseditome-modeleditome-stubsedit.gitmoduleseditbioformatseditome-jaieditome-poieditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 1313Triggerjob/Trigger/14e64b26a26ae6fffd9692b80136095535e7521cbce64b26a26ae6fffd9692b80136095535e7521cbcorigin/merge_cie64b26a26ae6fffd9692b80136095535e7521cbce64b26a26ae6fffd9692b80136095535e7521cbcorigin/merge_cie64b26a26ae6fffd9692b80136095535e7521cbce64b26a26ae6fffd9692b80136095535e7521cbcorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#14558996653283BIOFORMATS-image #1414falsefalse14468FAILURE1783988093108https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/14/docker6e3e8df3ee1e8d8654d09f47bba73d7285efeaff1783987270000https://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-javabioformats.gitmodulesome-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-onlyeditbio-formats-exampleseditbioformatseditome-mdbtoolseditome-stubseditZarrReadereditome-jaieditome-poieditbio-formats-documentationeditome-codecsedit.gitmoduleseditome-metakiteditome-modeleditome-common-javagithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 5050Triggerjob/Trigger/4336e3beba007496f2eca3578ef3e9b1410864afc036e3beba007496f2eca3578ef3e9b1410864afc0origin/merge_ci36e3beba007496f2eca3578ef3e9b1410864afc036e3beba007496f2eca3578ef3e9b1410864afc0origin/merge_ci36e3beba007496f2eca3578ef3e9b1410864afc036e3beba007496f2eca3578ef3e9b1410864afc0origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#43681729653283BIOFORMATS-image #4343falsefalse431218SUCCESS1786234533516https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/43/dockera1a6e99bc8e4275c759c4b8f58d70ab9364df5271786233681000https://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-onlyeditbio-formats-documentationeditome-codecseditome-common-javaeditbio-formats-exampleseditZarrReadereditome-mdbtoolseditome-modeleditome-stubsedit.gitmoduleseditbioformatseditome-jaieditome-poieditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 5050Triggerjob/Trigger/4336e3beba007496f2eca3578ef3e9b1410864afc036e3beba007496f2eca3578ef3e9b1410864afc0origin/merge_ci36e3beba007496f2eca3578ef3e9b1410864afc036e3beba007496f2eca3578ef3e9b1410864afc0origin/merge_ci36e3beba007496f2eca3578ef3e9b1410864afc036e3beba007496f2eca3578ef3e9b1410864afc0origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#43681729653283BIOFORMATS-image #4343falsefalse431218SUCCESS1786234533516https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/43/dockera1a6e99bc8e4275c759c4b8f58d70ab9364df5271786233681000https://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-onlyeditbio-formats-documentationeditome-codecseditome-common-javaeditbio-formats-exampleseditZarrReadereditome-mdbtoolseditome-modeleditome-stubsedit.gitmoduleseditbioformatseditome-jaieditome-poieditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopStarted by upstream project "Trigger" build number 1313Triggerjob/Trigger/14e64b26a26ae6fffd9692b80136095535e7521cbce64b26a26ae6fffd9692b80136095535e7521cbcorigin/merge_cie64b26a26ae6fffd9692b80136095535e7521cbce64b26a26ae6fffd9692b80136095535e7521cbcorigin/merge_cie64b26a26ae6fffd9692b80136095535e7521cbce64b26a26ae6fffd9692b80136095535e7521cbcorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#14558996653283BIOFORMATS-image #1414falsefalse14468FAILURE1783988093108https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-image/14/docker6e3e8df3ee1e8d8654d09f47bba73d7285efeaff1783987270000https://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-javabioformats.gitmodulesome-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-onlyeditbio-formats-exampleseditbioformatseditome-mdbtoolseditome-stubseditZarrReadereditome-jaieditome-poieditbio-formats-documentationeditome-codecsedit.gitmoduleseditome-metakiteditome-modeleditome-common-javagithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop44falsefalsedockerhudson.plugins.git.GitSCM--ffdefault