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161161BIOFORMATS-buildjob/BIOFORMATS-build/1617f19fb93cc859f512969e47a5ee6d5f4ba852fee7f19fb93cc859f512969e47a5ee6d5f4ba852feeorigin/merge_ci7f19fb93cc859f512969e47a5ee6d5f4ba852fee7f19fb93cc859f512969e47a5ee6d5f4ba852feeorigin/merge_ci7f19fb93cc859f512969e47a5ee6d5f4ba852fee7f19fb93cc859f512969e47a5ee6d5f4ba852feeorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildbio-formats-documentation-8.6.0-SNAPSHOT-documentation.tar.gzbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT-documentation.tar.gzbio-formats-documentation-8.6.0-SNAPSHOT-documentation.zipbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT-documentation.zipbio-formats-documentation-8.6.0-SNAPSHOT.jarbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT.jarbio-formats-examples-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bio-formats-examples/target/bio-formats-examples-8.6.0-SNAPSHOT-sources.jarbio-formats-examples-8.6.0-SNAPSHOT.jarbio-formats-build/bio-formats-examples/target/bio-formats-examples-8.6.0-SNAPSHOT.jarbio-formats_plugins-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT-sources.jarbio-formats_plugins-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT-tests.jarbio-formats_plugins-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT.jarbio-formats-tools-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT-sources.jarbio-formats-tools-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT-tests.jarbio-formats-tools-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT.jarbioformats_package-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bundles/bioformats_package/target/bioformats_package-8.6.0-SNAPSHOT.jarturbojpeg-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/forks/turbojpeg/target/turbojpeg-8.6.0-SNAPSHOT-sources.jarturbojpeg-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/forks/turbojpeg/target/turbojpeg-8.6.0-SNAPSHOT.jarformats-api-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT-sources.jarformats-api-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT-tests.jarformats-api-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT.jarformats-bsd-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT-sources.jarformats-bsd-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT-tests.jarformats-bsd-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT.jarformats-gpl-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT-sources.jarformats-gpl-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT-tests.jarformats-gpl-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT.jartest-suite-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT-sources.jartest-suite-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT-tests.jartest-suite-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT.jarome-codecs-1.1.4-SNAPSHOT-javadoc.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-javadoc.jarome-codecs-1.1.4-SNAPSHOT-sources.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-sources.jarome-codecs-1.1.4-SNAPSHOT-tests.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-tests.jarome-codecs-1.1.4-SNAPSHOT.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT.jarome-common-6.2.2-SNAPSHOT-javadoc.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-javadoc.jarome-common-6.2.2-SNAPSHOT-sources.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-sources.jarome-common-6.2.2-SNAPSHOT-tests.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-tests.jarome-common-6.2.2-SNAPSHOT.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT.jarome-jai-0.1.6-SNAPSHOT-javadoc.jarbio-formats-build/ome-jai/target/ome-jai-0.1.6-SNAPSHOT-javadoc.jarome-jai-0.1.6-SNAPSHOT-sources.jarbio-formats-build/ome-jai/target/ome-jai-0.1.6-SNAPSHO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» testintegration #161161falsefalse1616004SUCCESS1777075528701https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/161/testintegration0d01dafbf00bb54385c03153c43cba41a3bad8f51777075222000https://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#165 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/165/) 2026-04-25 00:00:22 +00000d01dafbf00bb54385c03153c43cba41a3bad8f5merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitb1d33604ef65a52c4136580b19c2bf27b24835341777075414000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#165 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/165/) 2026-04-25 00:03:34 +0000b1d33604ef65a52c4136580b19c2bf27b2483534merge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditome-jaieditZarrReadereditome-modeleditome-common-javaeditbio-formats-exampleseditome-codecsedit.gitmoduleseditome-metakiteditome-poieditome-mdbtoolseditome-stubseditbioformatsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit7f19fb93cc859f512969e47a5ee6d5f4ba852fee1777075518000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-25 00:05:18 +00007f19fb93cc859f512969e47a5ee6d5f4ba852feeUpdate component versionseditbio-formats-exampleseditbioformatseditome-codecseditome-poieditbio-formats-documentationeditome-modeleditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 160160BIOFORMATS-buildjob/BIOFORMATS-build/16058c592ca93d6a400b10f70aa30e17fcb62fa571958c592ca93d6a400b10f70aa30e17fcb62fa5719origin/merge_ci58c592ca93d6a400b10f70aa30e17fcb62fa571958c592ca93d6a400b10f70aa30e17fcb62fa5719origin/merge_ci58c592ca93d6a400b10f70aa30e17fcb62fa571958c592ca93d6a400b10f70aa30e17fcb62fa5719origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildbio-formats-documentation-8.6.0-SNAPSHOT-documentation.tar.gzbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT-documentation.tar.gzbio-formats-documentation-8.6.0-SNAPSHOT-documentation.zipbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT-documentation.zipbio-formats-documentation-8.6.0-SNAPSHOT.jarbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT.jarbio-formats-examples-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bio-formats-examples/target/bio-formats-examples-8.6.0-SNAPSHOT-sources.jarbio-formats-examples-8.6.0-SNAPSHOT.jarbio-formats-build/bio-formats-examples/target/bio-formats-examples-8.6.0-SNAPSHOT.jarbio-formats_plugins-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT-sources.jarbio-formats_plugins-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT-tests.jarbio-formats_plugins-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT.jarbio-formats-tools-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT-sources.jarbio-formats-tools-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT-tests.jarbio-formats-tools-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT.jarbioformats_package-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bundles/bioformats_package/target/bioformats_package-8.6.0-SNAPSHOT.jarturbojpeg-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/forks/turbojpeg/target/turbojpeg-8.6.0-SNAPSHOT-sources.jarturbojpeg-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/forks/turbojpeg/target/turbojpeg-8.6.0-SNAPSHOT.jarformats-api-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT-sources.jarformats-api-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT-tests.jarformats-api-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT.jarformats-bsd-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT-sources.jarformats-bsd-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT-tests.jarformats-bsd-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT.jarformats-gpl-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT-sources.jarformats-gpl-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT-tests.jarformats-gpl-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT.jartest-suite-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT-sources.jartest-suite-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT-tests.jartest-suite-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT.jarome-codecs-1.1.4-SNAPSHOT-javadoc.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-javadoc.jarome-codecs-1.1.4-SNAPSHOT-sources.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-sources.jarome-codecs-1.1.4-SNAPSHOT-tests.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-tests.jarome-codecs-1.1.4-SNAPSHOT.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT.jarome-common-6.2.2-SNAPSHOT-javadoc.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-javadoc.jarome-common-6.2.2-SNAPSHOT-sources.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-sources.jarome-common-6.2.2-SNAPSHOT-tests.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-tests.jarome-common-6.2.2-SNAPSHOT.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT.jarome-jai-0.1.6-SNAPSHOT-javadoc.jarbio-formats-build/ome-jai/target/ome-jai-0.1.6-SNAPSHOT-javadoc.jarome-jai-0.1.6-SNAPSHOT-sources.jarbio-formats-build/ome-jai/target/ome-jai-0.1.6-SNAPSHO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» testintegration #160160falsefalse1605959SUCCESS1776989121555https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/160/testintegrationfe9355b7d1d85e4eacb89515e840788ac72011ca1776988820000https://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#164 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/164/) 2026-04-24 00:00:20 +0000fe9355b7d1d85e4eacb89515e840788ac72011camerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitee02f37c7b18ae1e9a8ac5ec57c1df1669fcf20f1776989008000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#164 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/164/) 2026-04-24 00:03:28 +0000ee02f37c7b18ae1e9a8ac5ec57c1df1669fcf20fmerge master -Dorg -Ssuccess-onlyeditome-modeleditome-stubseditome-codecseditbio-formats-exampleseditZarrReadereditome-metakiteditbioformatseditome-poieditbio-formats-documentationeditome-mdbtoolseditome-common-javaedit.gitmoduleseditome-jaibioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit58c592ca93d6a400b10f70aa30e17fcb62fa57191776989113000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-24 00:05:13 +000058c592ca93d6a400b10f70aa30e17fcb62fa5719Update component versionseditome-metakiteditome-codecseditome-modeleditbio-formats-exampleseditome-poieditbio-formats-documentationeditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 159159BIOFORMATS-buildjob/BIOFORMATS-build/159b08cf72d16544889ba70f0e9cb859024ca8a5a86b08cf72d16544889ba70f0e9cb859024ca8a5a86origin/merge_cib08cf72d16544889ba70f0e9cb859024ca8a5a86b08cf72d16544889ba70f0e9cb859024ca8a5a86origin/merge_cib08cf72d16544889ba70f0e9cb859024ca8a5a86b08cf72d16544889ba70f0e9cb859024ca8a5a86origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildbio-formats-documentation-8.6.0-SNAPSHOT-documentation.tar.gzbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT-documentation.tar.gzbio-formats-documentation-8.6.0-SNAPSHOT-documentation.zipbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT-documentation.zipbio-formats-documentation-8.6.0-SNAPSHOT.jarbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT.jarbio-formats-examples-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bio-formats-examples/target/bio-formats-examples-8.6.0-SNAPSHOT-sources.jarbio-formats-examples-8.6.0-SNAPSHOT.jarbio-formats-build/bio-formats-examples/target/bio-formats-examples-8.6.0-SNAPSHOT.jarbio-formats_plugins-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT-sources.jarbio-formats_plugins-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT-tests.jarbio-formats_plugins-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT.jarbio-formats-tools-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT-sources.jarbio-formats-tools-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT-tests.jarbio-formats-tools-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT.jarbioformats_package-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bundles/bioformats_package/target/bioformats_package-8.6.0-SNAPSHOT.jarturbojpeg-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/forks/turbojpeg/target/turbojpeg-8.6.0-SNAPSHOT-sources.jarturbojpeg-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/forks/turbojpeg/target/turbojpeg-8.6.0-SNAPSHOT.jarformats-api-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT-sources.jarformats-api-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT-tests.jarformats-api-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT.jarformats-bsd-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT-sources.jarformats-bsd-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT-tests.jarformats-bsd-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT.jarformats-gpl-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT-sources.jarformats-gpl-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT-tests.jarformats-gpl-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT.jartest-suite-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT-sources.jartest-suite-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT-tests.jartest-suite-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT.jarome-codecs-1.1.4-SNAPSHOT-javadoc.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-javadoc.jarome-codecs-1.1.4-SNAPSHOT-sources.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-sources.jarome-codecs-1.1.4-SNAPSHOT-tests.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-tests.jarome-codecs-1.1.4-SNAPSHOT.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT.jarome-common-6.2.2-SNAPSHOT-javadoc.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-javadoc.jarome-common-6.2.2-SNAPSHOT-sources.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-sources.jarome-common-6.2.2-SNAPSHOT-tests.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-tests.jarome-common-6.2.2-SNAPSHOT.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT.jarome-jai-0.1.6-SNAPSHOT-javadoc.jarbio-formats-build/ome-jai/target/ome-jai-0.1.6-SNAPSHOT-javadoc.jarome-jai-0.1.6-SNAPSHOT-sources.jarbio-formats-build/ome-jai/target/ome-jai-0.1.6-SNAPSHO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» testintegration #159159falsefalse1595914SUCCESS1776952525618https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/159/testintegrationd82cf42fbfc438f33c58b71ea90c218b48c72e8e1776952200000https://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#163 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/163/) 2026-04-23 13:50:00 +0000d82cf42fbfc438f33c58b71ea90c218b48c72e8emerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitceea4b26283f9e8a011ba4e658b701ed78c5b2621776952409000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#163 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/163/) 2026-04-23 13:53:29 +0000ceea4b26283f9e8a011ba4e658b701ed78c5b262merge master -Dorg -Ssuccess-onlyeditome-jaieditome-stubseditbio-formats-documentationeditome-modeleditome-metakiteditZarrReaderedit.gitmoduleseditome-codecseditome-common-javaeditbio-formats-exampleseditbioformatseditome-poieditome-mdbtoolsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitb08cf72d16544889ba70f0e9cb859024ca8a5a861776952514000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-23 13:55:14 +0000b08cf72d16544889ba70f0e9cb859024ca8a5a86Update component versionseditbioformatseditome-metakiteditome-modeleditome-poieditome-codecseditbio-formats-exampleseditbio-formats-documentationgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 158158BIOFORMATS-buildjob/BIOFORMATS-build/158ff798ce078d437c48dd4239b04c3afb702d0cab7ff798ce078d437c48dd4239b04c3afb702d0cab7origin/merge_ciff798ce078d437c48dd4239b04c3afb702d0cab7ff798ce078d437c48dd4239b04c3afb702d0cab7origin/merge_ciff798ce078d437c48dd4239b04c3afb702d0cab7ff798ce078d437c48dd4239b04c3afb702d0cab7origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildbio-formats-documentation-8.6.0-SNAPSHOT-documentation.tar.gzbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT-documentation.tar.gzbio-formats-documentation-8.6.0-SNAPSHOT-documentation.zipbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT-documentation.zipbio-formats-documentation-8.6.0-SNAPSHOT.jarbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT.jarbio-formats-examples-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bio-formats-examples/target/bio-formats-examples-8.6.0-SNAPSHOT-sources.jarbio-formats-examples-8.6.0-SNAPSHOT.jarbio-formats-build/bio-formats-examples/target/bio-formats-examples-8.6.0-SNAPSHOT.jarbio-formats_plugins-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT-sources.jarbio-formats_plugins-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT-tests.jarbio-formats_plugins-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT.jarbio-formats-tools-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT-sources.jarbio-formats-tools-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT-tests.jarbio-formats-tools-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT.jarbioformats_package-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bundles/bioformats_package/target/bioformats_package-8.6.0-SNAPSHOT.jarturbojpeg-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/forks/turbojpeg/target/turbojpeg-8.6.0-SNAPSHOT-sources.jarturbojpeg-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/forks/turbojpeg/target/turbojpeg-8.6.0-SNAPSHOT.jarformats-api-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT-sources.jarformats-api-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT-tests.jarformats-api-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT.jarformats-bsd-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT-sources.jarformats-bsd-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT-tests.jarformats-bsd-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT.jarformats-gpl-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT-sources.jarformats-gpl-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT-tests.jarformats-gpl-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT.jartest-suite-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT-sources.jartest-suite-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT-tests.jartest-suite-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT.jarome-codecs-1.1.4-SNAPSHOT-javadoc.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-javadoc.jarome-codecs-1.1.4-SNAPSHOT-sources.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-sources.jarome-codecs-1.1.4-SNAPSHOT-tests.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-tests.jarome-codecs-1.1.4-SNAPSHOT.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT.jarome-common-6.2.2-SNAPSHOT-javadoc.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-javadoc.jarome-common-6.2.2-SNAPSHOT-sources.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-sources.jarome-common-6.2.2-SNAPSHOT-tests.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-tests.jarome-common-6.2.2-SNAPSHOT.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT.jarome-jai-0.1.6-SNAPSHOT-javadoc.jarbio-formats-build/ome-jai/target/ome-jai-0.1.6-SNAPSHOT-javadoc.jarome-jai-0.1.6-SNAPSHOT-sources.jarbio-formats-build/ome-jai/target/ome-jai-0.1.6-SNAPSHO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» testintegration #158158falsefalse1585889SUCCESS1776948695502https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/158/testintegrationd4943e5140fb263127ffcdca0b7d15775dd12fac1776948378000https://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#162 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/162/) 2026-04-23 12:46:18 +0000d4943e5140fb263127ffcdca0b7d15775dd12facmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit026093b675804bc5f0c14f53c1b8b1e16eb3c8c61776948579000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#162 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/162/) 2026-04-23 12:49:39 +0000026093b675804bc5f0c14f53c1b8b1e16eb3c8c6merge master -Dorg -Ssuccess-onlyeditome-poieditome-common-javaeditZarrReadereditbioformatseditome-mdbtoolseditome-stubseditome-jaieditbio-formats-exampleseditome-metakiteditome-modeledit.gitmoduleseditome-codecseditbio-formats-documentationbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitff798ce078d437c48dd4239b04c3afb702d0cab71776948684000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-23 12:51:24 +0000ff798ce078d437c48dd4239b04c3afb702d0cab7Update component versionseditome-modeleditome-poieditome-codecseditbioformatseditbio-formats-documentationeditome-metakiteditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 157157BIOFORMATS-buildjob/BIOFORMATS-build/157fb64b1f422188d0bb06b0bd6a9f9f50b2528a5b3fb64b1f422188d0bb06b0bd6a9f9f50b2528a5b3origin/merge_cifb64b1f422188d0bb06b0bd6a9f9f50b2528a5b3fb64b1f422188d0bb06b0bd6a9f9f50b2528a5b3origin/merge_cifb64b1f422188d0bb06b0bd6a9f9f50b2528a5b3fb64b1f422188d0bb06b0bd6a9f9f50b2528a5b3origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#157129791128153BIOFORMATS-build » testintegration #157157falsefalse1575873SUCCESS1776947000445https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/157/testintegration5956451c811de49cd3fcc1cc5794984c61146d461776946679000https://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#161 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/161/) 2026-04-23 12:17:59 +00005956451c811de49cd3fcc1cc5794984c61146d46merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakita2d8644571928f7d39e919a4a94bb20c92dede5d1776946887000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#161 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/161/) 2026-04-23 12:21:27 +0000a2d8644571928f7d39e919a4a94bb20c92dede5dmerge master -Dorg -Ssuccess-onlyeditbioformatseditome-jaieditbio-formats-exampleseditome-mdbtoolseditome-codecseditome-metakiteditome-stubseditome-poieditome-modeleditome-common-javaeditZarrReadereditbio-formats-documentationedit.gitmodulesbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitfb64b1f422188d0bb06b0bd6a9f9f50b2528a5b31776946992000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-23 12:23:12 +0000fb64b1f422188d0bb06b0bd6a9f9f50b2528a5b3Update component versionseditbio-formats-documentationeditbio-formats-exampleseditome-metakiteditbioformatseditome-modeleditome-poieditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 156156BIOFORMATS-buildjob/BIOFORMATS-build/15656d3ee22aa100c22dd1c985a10d96976a980706456d3ee22aa100c22dd1c985a10d96976a9807064origin/merge_ci56d3ee22aa100c22dd1c985a10d96976a980706456d3ee22aa100c22dd1c985a10d96976a9807064origin/merge_ci56d3ee22aa100c22dd1c985a10d96976a980706456d3ee22aa100c22dd1c985a10d96976a9807064origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#156131317128153BIOFORMATS-build » testintegration #156156falsefalse1565830SUCCESS1776933885059https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/156/testintegration564d09e81daf9e87fcef817f175e02e5ee09d6541776933568000https://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#160 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/160/) 2026-04-23 08:39:28 +0000564d09e81daf9e87fcef817f175e02e5ee09d654merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit4f7fe3b1af9350cf5728eb3fba045c2961d26de91776933770000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#160 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/160/) 2026-04-23 08:42:50 +00004f7fe3b1af9350cf5728eb3fba045c2961d26de9merge master -Dorg -Ssuccess-onlyeditome-modeleditome-poieditome-metakiteditbio-formats-documentationeditZarrReadereditome-codecseditbio-formats-exampleseditbioformatseditome-stubsedit.gitmoduleseditome-jaieditome-common-javaeditome-mdbtoolsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit56d3ee22aa100c22dd1c985a10d96976a98070641776933874000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-23 08:44:34 +000056d3ee22aa100c22dd1c985a10d96976a9807064Update component versionseditbioformatseditome-modeleditome-codecseditbio-formats-exampleseditome-metakiteditbio-formats-documentationeditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 155155BIOFORMATS-buildjob/BIOFORMATS-build/155e7f05d7573b34e3f38d678daef062cd90dec70f5e7f05d7573b34e3f38d678daef062cd90dec70f5origin/merge_cie7f05d7573b34e3f38d678daef062cd90dec70f5e7f05d7573b34e3f38d678daef062cd90dec70f5origin/merge_cie7f05d7573b34e3f38d678daef062cd90dec70f5e7f05d7573b34e3f38d678daef062cd90dec70f5origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#155138214128153BIOFORMATS-build » testintegration #155155falsefalse1555819SUCCESS1776931769993https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/155/testintegration35687ac707c5f5b616009836b4e794581a3b92ec1776931458000https://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#159 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/159/) 2026-04-23 08:04:18 +000035687ac707c5f5b616009836b4e794581a3b92ecmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit85ad5d88b53a5533d17ab2431ed1ee4b576ada251776931657000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#159 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/159/) 2026-04-23 08:07:37 +000085ad5d88b53a5533d17ab2431ed1ee4b576ada25merge master -Dorg -Ssuccess-onlyeditome-poieditZarrReadereditome-stubseditbioformatseditome-mdbtoolsedit.gitmoduleseditome-modeleditome-common-javaeditome-metakiteditbio-formats-documentationeditbio-formats-exampleseditome-jaieditome-codecsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakite7f05d7573b34e3f38d678daef062cd90dec70f51776931762000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-23 08:09:22 +0000e7f05d7573b34e3f38d678daef062cd90dec70f5Update component versionseditome-codecseditome-modeleditbio-formats-exampleseditbio-formats-documentationeditbioformatseditome-metakiteditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 154154BIOFORMATS-buildjob/BIOFORMATS-build/15469e5780284ad87cd7b27ae0eb80e978def81b17169e5780284ad87cd7b27ae0eb80e978def81b171origin/merge_ci69e5780284ad87cd7b27ae0eb80e978def81b17169e5780284ad87cd7b27ae0eb80e978def81b171origin/merge_ci69e5780284ad87cd7b27ae0eb80e978def81b17169e5780284ad87cd7b27ae0eb80e978def81b171origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#154134724128153BIOFORMATS-build » testintegration #154154falsefalse1545808SUCCESS1776902729199https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/154/testintegration1552dbe524de766c82cf2c7c96d96ef9cc7d2d8f1776902422000https://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#158 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/158/) 2026-04-23 00:00:22 +00001552dbe524de766c82cf2c7c96d96ef9cc7d2d8fmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitce3c18e2fe06f9db8785ec9fd6ff05cb72574bf61776902615000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#158 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/158/) 2026-04-23 00:03:35 +0000ce3c18e2fe06f9db8785ec9fd6ff05cb72574bf6merge master -Dorg -Ssuccess-onlyeditome-modeleditome-common-javaeditome-poiedit.gitmoduleseditZarrReadereditome-codecseditbioformatseditome-metakiteditome-jaieditbio-formats-exampleseditbio-formats-documentationeditome-mdbtoolseditome-stubsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit69e5780284ad87cd7b27ae0eb80e978def81b1711776902720000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-23 00:05:20 +000069e5780284ad87cd7b27ae0eb80e978def81b171Update component versionseditome-modeleditome-poieditbio-formats-exampleseditbioformatseditbio-formats-documentationeditome-metakiteditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 153153BIOFORMATS-buildjob/BIOFORMATS-build/153ffe0763082d0ae9924fd2f62986c6da82384d3c7ffe0763082d0ae9924fd2f62986c6da82384d3c7origin/merge_ciffe0763082d0ae9924fd2f62986c6da82384d3c7ffe0763082d0ae9924fd2f62986c6da82384d3c7origin/merge_ciffe0763082d0ae9924fd2f62986c6da82384d3c7ffe0763082d0ae9924fd2f62986c6da82384d3c7origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#153134593128153BIOFORMATS-build » testintegration #153153falsefalse1535781SUCCESS1776855852861https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/153/testintegration0f6ce851de7d7aa968962ca2d6793734e07ac32f1776855546000https://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#157 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/157/) 2026-04-22 10:59:06 +00000f6ce851de7d7aa968962ca2d6793734e07ac32fmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit4df1a7ecad5e8f59702646f642691ccf5fbc377a1776855742000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#157 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/157/) 2026-04-22 11:02:22 +00004df1a7ecad5e8f59702646f642691ccf5fbc377amerge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditbioformatseditome-poieditome-codecseditome-modeleditome-mdbtoolseditZarrReaderedit.gitmoduleseditome-common-javaeditbio-formats-documentationeditome-stubseditome-jaieditome-metakitbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitffe0763082d0ae9924fd2f62986c6da82384d3c71776855844000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-22 11:04:04 +0000ffe0763082d0ae9924fd2f62986c6da82384d3c7Update component versionseditome-poieditome-metakiteditbioformatseditome-modeleditbio-formats-exampleseditome-codecseditbio-formats-documentationgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 152152BIOFORMATS-buildjob/BIOFORMATS-build/152bc3bf37b6534a69ed8440f18677cf1f2e66f7d8ebc3bf37b6534a69ed8440f18677cf1f2e66f7d8eorigin/merge_cibc3bf37b6534a69ed8440f18677cf1f2e66f7d8ebc3bf37b6534a69ed8440f18677cf1f2e66f7d8eorigin/merge_cibc3bf37b6534a69ed8440f18677cf1f2e66f7d8ebc3bf37b6534a69ed8440f18677cf1f2e66f7d8eorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#152220071128153BIOFORMATS-build » testintegration #152152falsefalse1525760SUCCESS1776849577631https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/152/testintegrationb16ad1cd6dc55b632359e2de0e087bb99abb68cf1776849249000https://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#156 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/156/) 2026-04-22 09:14:09 +0000b16ad1cd6dc55b632359e2de0e087bb99abb68cfmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitd34979bc3a9a4c653584040db77a77f9d297258f1776849453000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#156 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/156/) 2026-04-22 09:17:33 +0000d34979bc3a9a4c653584040db77a77f9d297258fmerge master -Dorg -Ssuccess-onlyedit.gitmoduleseditome-codecseditome-mdbtoolseditome-metakiteditome-modeleditbioformatseditome-jaieditZarrReadereditome-poieditome-common-javaeditbio-formats-documentationeditome-stubseditbio-formats-examplesbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitbc3bf37b6534a69ed8440f18677cf1f2e66f7d8e1776849568000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-22 09:19:28 +0000bc3bf37b6534a69ed8440f18677cf1f2e66f7d8eUpdate component versionseditome-poieditbio-formats-documentationeditbio-formats-exampleseditbioformatseditome-modeleditome-metakiteditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 151151BIOFORMATS-buildjob/BIOFORMATS-build/151e643f765057fcc1b929b67e76f81a6214eaae02fe643f765057fcc1b929b67e76f81a6214eaae02forigin/merge_cie643f765057fcc1b929b67e76f81a6214eaae02fe643f765057fcc1b929b67e76f81a6214eaae02forigin/merge_cie643f765057fcc1b929b67e76f81a6214eaae02fe643f765057fcc1b929b67e76f81a6214eaae02forigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#151127075128153BIOFORMATS-build » testintegration #151151falsefalse1515701SUCCESS1776729927566https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/151/testintegrationa6ed2132bb2ec71386d50076613d17afac85628b1776729622000https://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#155 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/155/) 2026-04-21 00:00:22 +0000a6ed2132bb2ec71386d50076613d17afac85628bmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit25c3995d89ddc227e9c8120afb3b0c98cdafa0911776729815000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#155 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/155/) 2026-04-21 00:03:35 +000025c3995d89ddc227e9c8120afb3b0c98cdafa091merge master -Dorg -Ssuccess-onlyeditome-modeledit.gitmoduleseditbio-formats-documentationeditome-mdbtoolseditome-jaieditbioformatseditbio-formats-exampleseditome-poieditome-metakiteditome-stubseditome-codecseditZarrReadereditome-common-javabioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakite643f765057fcc1b929b67e76f81a6214eaae02f1776729918000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-21 00:05:18 +0000e643f765057fcc1b929b67e76f81a6214eaae02fUpdate component versionseditome-codecseditbioformatseditome-modeleditome-poieditbio-formats-exampleseditome-metakiteditbio-formats-documentationgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 150150BIOFORMATS-buildjob/BIOFORMATS-build/15021a565db4df7d54c22cbca24bf035a04bee00f8321a565db4df7d54c22cbca24bf035a04bee00f83origin/merge_ci21a565db4df7d54c22cbca24bf035a04bee00f8321a565db4df7d54c22cbca24bf035a04bee00f83origin/merge_ci21a565db4df7d54c22cbca24bf035a04bee00f8321a565db4df7d54c22cbca24bf035a04bee00f83origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#150129393128153BIOFORMATS-build » testintegration #150150falsefalse1505656SUCCESS1776674436197https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/150/testintegrationd3911da2425b825d57b6b84034077d441d704ee21776674104000https://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#154 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/154/) 2026-04-20 08:35:04 +0000d3911da2425b825d57b6b84034077d441d704ee2merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakita28b45e638d57317ba6310b5ca6f84186a49a76a1776674324000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#154 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/154/) 2026-04-20 08:38:44 +0000a28b45e638d57317ba6310b5ca6f84186a49a76amerge master -Dorg -Ssuccess-onlyeditome-metakiteditome-poieditome-jaieditome-common-javaeditbio-formats-documentationeditome-codecseditome-mdbtoolseditome-stubsedit.gitmoduleseditome-modeleditZarrReadereditbio-formats-exampleseditbioformatsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit21a565db4df7d54c22cbca24bf035a04bee00f831776674427000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-20 08:40:27 +000021a565db4df7d54c22cbca24bf035a04bee00f83Update component versionseditbio-formats-documentationeditbioformatseditome-modeleditome-metakiteditbio-formats-exampleseditome-codecseditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 149149BIOFORMATS-buildjob/BIOFORMATS-build/1495ec20d254598d14d3ad2b6c4843c54d43deb39665ec20d254598d14d3ad2b6c4843c54d43deb3966origin/merge_ci5ec20d254598d14d3ad2b6c4843c54d43deb39665ec20d254598d14d3ad2b6c4843c54d43deb3966origin/merge_ci5ec20d254598d14d3ad2b6c4843c54d43deb39665ec20d254598d14d3ad2b6c4843c54d43deb3966origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#149131304128153BIOFORMATS-build » testintegration #149149falsefalse1495623SUCCESS1776643525431https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/149/testintegrationb5ba2e572035bafe5888e5bac535a91e04e13cc01776643223000https://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#153 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/153/) 2026-04-20 00:00:23 +0000b5ba2e572035bafe5888e5bac535a91e04e13cc0merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitb3da4350f34d01b3661e548063b493d7ed6e18d01776643412000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#153 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/153/) 2026-04-20 00:03:32 +0000b3da4350f34d01b3661e548063b493d7ed6e18d0merge master -Dorg -Ssuccess-onlyeditome-codecseditbio-formats-exampleseditome-poieditome-mdbtoolseditbio-formats-documentationeditbioformatseditome-metakiteditome-common-javaeditome-jaiedit.gitmoduleseditome-stubseditome-modeleditZarrReaderbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit5ec20d254598d14d3ad2b6c4843c54d43deb39661776643513000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-20 00:05:13 +00005ec20d254598d14d3ad2b6c4843c54d43deb3966Update component versionseditbioformatseditome-codecseditome-metakiteditome-modeleditbio-formats-documentationeditome-poieditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 148148BIOFORMATS-buildjob/BIOFORMATS-build/1485ad651d2a3a9d47c2f68809e238cf324573081625ad651d2a3a9d47c2f68809e238cf32457308162origin/merge_ci5ad651d2a3a9d47c2f68809e238cf324573081625ad651d2a3a9d47c2f68809e238cf32457308162origin/merge_ci5ad651d2a3a9d47c2f68809e238cf324573081625ad651d2a3a9d47c2f68809e238cf32457308162origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#148131462128153BIOFORMATS-build » testintegration #148148falsefalse1485608SUCCESS1776557118402https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/148/testintegration276302ca95b10361a3e08329a4163dc1b880fde71776556822000https://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#152 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/152/) 2026-04-19 00:00:22 +0000276302ca95b10361a3e08329a4163dc1b880fde7merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitf5a3f5ded24a213cc3ff2a5143cc818cbc5865911776557008000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#152 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/152/) 2026-04-19 00:03:28 +0000f5a3f5ded24a213cc3ff2a5143cc818cbc586591merge master -Dorg -Ssuccess-onlyeditome-stubseditome-jaieditome-common-javaedit.gitmoduleseditbio-formats-exampleseditbioformatseditome-metakiteditome-codecseditome-mdbtoolseditbio-formats-documentationeditome-modeleditome-poieditZarrReaderbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit5ad651d2a3a9d47c2f68809e238cf324573081621776557107000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-19 00:05:07 +00005ad651d2a3a9d47c2f68809e238cf32457308162Update component versionseditbioformatseditome-metakiteditome-modeleditome-codecseditbio-formats-exampleseditbio-formats-documentationeditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 147147BIOFORMATS-buildjob/BIOFORMATS-build/14763c6b253733e6048f3749ab8e99e3537e7cf8d3a63c6b253733e6048f3749ab8e99e3537e7cf8d3aorigin/merge_ci63c6b253733e6048f3749ab8e99e3537e7cf8d3a63c6b253733e6048f3749ab8e99e3537e7cf8d3aorigin/merge_ci63c6b253733e6048f3749ab8e99e3537e7cf8d3a63c6b253733e6048f3749ab8e99e3537e7cf8d3aorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#147130448128153BIOFORMATS-build » testintegration #147147falsefalse1475579SUCCESS1776490141799https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/147/testintegrationa5561a14c169c0040888282711eb82984c050bb01776489855000https://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#151 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/151/) 2026-04-18 05:24:15 +0000a5561a14c169c0040888282711eb82984c050bb0merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit4179a2693dd672f75d5b359618014da54db4d8371776490036000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#151 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/151/) 2026-04-18 05:27:16 +00004179a2693dd672f75d5b359618014da54db4d837merge master -Dorg -Ssuccess-onlyeditome-stubseditZarrReadereditbioformatseditbio-formats-examplesedit.gitmoduleseditome-codecseditome-poieditome-modeleditbio-formats-documentationeditome-jaieditome-metakiteditome-mdbtoolseditome-common-javabioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit63c6b253733e6048f3749ab8e99e3537e7cf8d3a1776490134000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-18 05:28:54 +000063c6b253733e6048f3749ab8e99e3537e7cf8d3aUpdate component versionseditbio-formats-exampleseditome-metakiteditbio-formats-documentationeditome-poieditbioformatseditome-codecseditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 146146BIOFORMATS-buildjob/BIOFORMATS-build/146100df00e95385ce7c9b079eb287fa46c742b840f100df00e95385ce7c9b079eb287fa46c742b840forigin/merge_ci100df00e95385ce7c9b079eb287fa46c742b840f100df00e95385ce7c9b079eb287fa46c742b840forigin/merge_ci100df00e95385ce7c9b079eb287fa46c742b840f100df00e95385ce7c9b079eb287fa46c742b840forigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#146130293128153BIOFORMATS-build » testintegration #146146falsefalse1465566SUCCESS1776470716299https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/146/testintegration0b3c72b75a907b5ea24b6796a6f82f02f7c17e511776470419000https://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#150 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/150/) 2026-04-18 00:00:19 +00000b3c72b75a907b5ea24b6796a6f82f02f7c17e51merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit1c4b53031cfd752c429e1e5eb4829bb5eb261a251776470608000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#150 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/150/) 2026-04-18 00:03:28 +00001c4b53031cfd752c429e1e5eb4829bb5eb261a25merge master -Dorg -Ssuccess-onlyeditome-poieditome-mdbtoolsedit.gitmoduleseditome-common-javaeditome-modeleditZarrReadereditome-jaieditbio-formats-exampleseditbio-formats-documentationeditome-metakiteditome-stubseditome-codecseditbioformatsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit100df00e95385ce7c9b079eb287fa46c742b840f1776470708000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-18 00:05:08 +0000100df00e95385ce7c9b079eb287fa46c742b840fUpdate component versionseditome-poieditome-codecseditbio-formats-documentationeditbioformatseditbio-formats-exampleseditome-modeleditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 145145BIOFORMATS-buildjob/BIOFORMATS-build/14561969583bf14e97516a5fc5c00789aa92daccff561969583bf14e97516a5fc5c00789aa92daccff5origin/merge_ci61969583bf14e97516a5fc5c00789aa92daccff561969583bf14e97516a5fc5c00789aa92daccff5origin/merge_ci61969583bf14e97516a5fc5c00789aa92daccff561969583bf14e97516a5fc5c00789aa92daccff5origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#145131249128153BIOFORMATS-build » testintegration #145145falsefalse1455553SUCCESS1776430165307https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/145/testintegrationf49f90a70b3eae3cca08e9b18cd933ed13116c831776429864000https://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#149 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/149/) 2026-04-17 12:44:24 +0000f49f90a70b3eae3cca08e9b18cd933ed13116c83merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit926b3194727b01351abc39795a46431f13a1a8d41776430057000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#149 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/149/) 2026-04-17 12:47:37 +0000926b3194727b01351abc39795a46431f13a1a8d4merge master -Dorg -Ssuccess-onlyeditome-common-javaeditbio-formats-documentationeditome-poieditZarrReadereditbioformatseditome-jaieditome-stubseditome-modeleditome-codecseditome-metakitedit.gitmoduleseditbio-formats-exampleseditome-mdbtoolsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit61969583bf14e97516a5fc5c00789aa92daccff51776430155000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-17 12:49:15 +000061969583bf14e97516a5fc5c00789aa92daccff5Update component versionseditome-metakiteditbio-formats-exampleseditbio-formats-documentationeditome-codecseditome-modeleditbioformatseditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 144144BIOFORMATS-buildjob/BIOFORMATS-build/144c4804c242f0e0c115020725d0dcd102ab1f6c9dfc4804c242f0e0c115020725d0dcd102ab1f6c9dforigin/merge_cic4804c242f0e0c115020725d0dcd102ab1f6c9dfc4804c242f0e0c115020725d0dcd102ab1f6c9dforigin/merge_cic4804c242f0e0c115020725d0dcd102ab1f6c9dfc4804c242f0e0c115020725d0dcd102ab1f6c9dforigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#144128608128153BIOFORMATS-build » testintegration #144144falsefalse1445540SUCCESS1776428500256https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/144/testintegration622dfc5c520eb6e2f823a59e1b34b6a6cb02e2e51776428194000https://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#148 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/148/) 2026-04-17 12:16:34 +0000622dfc5c520eb6e2f823a59e1b34b6a6cb02e2e5merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitd33e526467432ad9625cb21f09b81ed8952ad7b51776428391000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#148 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/148/) 2026-04-17 12:19:51 +0000d33e526467432ad9625cb21f09b81ed8952ad7b5merge master -Dorg -Ssuccess-onlyeditome-stubseditome-poieditome-codecseditome-metakiteditZarrReadereditome-common-javaedit.gitmoduleseditome-mdbtoolseditbio-formats-exampleseditome-jaieditbio-formats-documentationeditome-modeleditbioformatsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitc4804c242f0e0c115020725d0dcd102ab1f6c9df1776428489000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-17 12:21:29 +0000c4804c242f0e0c115020725d0dcd102ab1f6c9dfUpdate component versionseditbio-formats-documentationeditome-codecseditome-metakiteditome-modeleditbioformatseditome-poieditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 143143BIOFORMATS-buildjob/BIOFORMATS-build/143386396284368ccf3347afb3ec6cb59211bbc03bd386396284368ccf3347afb3ec6cb59211bbc03bdorigin/merge_ci386396284368ccf3347afb3ec6cb59211bbc03bd386396284368ccf3347afb3ec6cb59211bbc03bdorigin/merge_ci386396284368ccf3347afb3ec6cb59211bbc03bd386396284368ccf3347afb3ec6cb59211bbc03bdorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#143132490128153BIOFORMATS-build » testintegration #143143falsefalse1435527SUCCESS1776426190186https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/143/testintegration9d21494d89d63304cc1342bbff97a0e6614eba961776425889000https://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#147 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/147/) 2026-04-17 11:38:09 +00009d21494d89d63304cc1342bbff97a0e6614eba96merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit398228b49758a0b1b512039e5e60dbbe531a85991776426079000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#147 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/147/) 2026-04-17 11:41:19 +0000398228b49758a0b1b512039e5e60dbbe531a8599merge master -Dorg -Ssuccess-onlyeditome-metakiteditome-poieditome-stubseditome-jaieditome-modeleditbioformatseditome-common-javaeditome-mdbtoolseditbio-formats-exampleseditbio-formats-documentationeditome-codecseditZarrReaderedit.gitmodulesbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit386396284368ccf3347afb3ec6cb59211bbc03bd1776426178000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-17 11:42:58 +0000386396284368ccf3347afb3ec6cb59211bbc03bdUpdate component versionseditome-modeleditome-poieditbio-formats-documentationeditbio-formats-exampleseditbioformatseditome-codecseditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 142142BIOFORMATS-buildjob/BIOFORMATS-build/142c483a2f85a989ac023d8ca73f2c9a70d510211b2c483a2f85a989ac023d8ca73f2c9a70d510211b2origin/merge_cic483a2f85a989ac023d8ca73f2c9a70d510211b2c483a2f85a989ac023d8ca73f2c9a70d510211b2origin/merge_cic483a2f85a989ac023d8ca73f2c9a70d510211b2c483a2f85a989ac023d8ca73f2c9a70d510211b2origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#142131410128153BIOFORMATS-build » testintegration #142142falsefalse1425499SUCCESS1776422190070https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/142/testintegrationd1e159990efd53fe5960d35b40c3e40756d2dfc51776421888000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#146 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/146/) 2026-04-17 10:31:28 +0000d1e159990efd53fe5960d35b40c3e40756d2dfc5merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit00ab1487af31f642c52cdf6e70fef110423b03ad1776422079000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#146 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/146/) 2026-04-17 10:34:39 +000000ab1487af31f642c52cdf6e70fef110423b03admerge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditome-modeledit.gitmoduleseditome-codecseditome-mdbtoolseditome-poieditome-stubseditome-common-javaeditbio-formats-exampleseditome-metakiteditome-jaieditbioformatseditZarrReaderbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitc483a2f85a989ac023d8ca73f2c9a70d510211b21776422179000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-17 10:36:19 +0000c483a2f85a989ac023d8ca73f2c9a70d510211b2Update component versionseditbio-formats-documentationeditbio-formats-exampleseditome-metakiteditbioformatseditome-poieditome-modeleditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 141141BIOFORMATS-buildjob/BIOFORMATS-build/1413adc0b3ef6d3ea2975c07d63b0c464ad936c40f03adc0b3ef6d3ea2975c07d63b0c464ad936c40f0origin/merge_ci3adc0b3ef6d3ea2975c07d63b0c464ad936c40f03adc0b3ef6d3ea2975c07d63b0c464ad936c40f0origin/merge_ci3adc0b3ef6d3ea2975c07d63b0c464ad936c40f03adc0b3ef6d3ea2975c07d63b0c464ad936c40f0origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#141131270128153BIOFORMATS-build » testintegration #141141falsefalse1415462SUCCESS1776413734843https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/141/testintegration39850c27b34670288b87e674e54ed214c74023bb1776413434000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#145 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/145/) 2026-04-17 08:10:34 +000039850c27b34670288b87e674e54ed214c74023bbmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit4dfbb9f4df24f6336376b4a6b4986f04c6b9d1091776413627000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#145 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/145/) 2026-04-17 08:13:47 +00004dfbb9f4df24f6336376b4a6b4986f04c6b9d109merge master -Dorg -Ssuccess-onlyeditZarrReadereditome-mdbtoolseditome-stubseditbio-formats-exampleseditbio-formats-documentationeditome-common-javaeditome-metakiteditome-poiedit.gitmoduleseditome-codecseditbioformatseditome-jaieditome-modelbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit3adc0b3ef6d3ea2975c07d63b0c464ad936c40f01776413727000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-17 08:15:27 +00003adc0b3ef6d3ea2975c07d63b0c464ad936c40f0Update component versionseditome-codecseditome-modeleditbio-formats-documentationeditome-poieditbio-formats-exampleseditome-metakiteditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 140140BIOFORMATS-buildjob/BIOFORMATS-build/14006ea8330a0dafd130dfd65b4845743f79dd6045a06ea8330a0dafd130dfd65b4845743f79dd6045aorigin/merge_ci06ea8330a0dafd130dfd65b4845743f79dd6045a06ea8330a0dafd130dfd65b4845743f79dd6045aorigin/merge_ci06ea8330a0dafd130dfd65b4845743f79dd6045a06ea8330a0dafd130dfd65b4845743f79dd6045aorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#140129337128153BIOFORMATS-build » testintegration #140140falsefalse1405437SUCCESS1776409629721https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/140/testintegration56834dfef72307f4cf28beabf67c7ccc54ef41121776409318000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#144 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/144/) 2026-04-17 07:01:58 +000056834dfef72307f4cf28beabf67c7ccc54ef4112merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakite3cd167ef4a168e4febc2fbfd4091591f17fb3101776409518000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#144 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/144/) 2026-04-17 07:05:18 +0000e3cd167ef4a168e4febc2fbfd4091591f17fb310merge master -Dorg -Ssuccess-onlyeditome-metakiteditome-codecseditome-common-javaeditome-stubseditome-mdbtoolseditbio-formats-examplesedit.gitmoduleseditome-poieditZarrReadereditbio-formats-documentationeditbioformatseditome-jaieditome-modelbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit06ea8330a0dafd130dfd65b4845743f79dd6045a1776409620000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-17 07:07:00 +000006ea8330a0dafd130dfd65b4845743f79dd6045aUpdate component versionseditbio-formats-documentationeditome-modeleditome-codecseditbioformatseditome-poieditome-metakiteditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 139139BIOFORMATS-buildjob/BIOFORMATS-build/139a6e4c54282ae7a1af89b9d2a8b2241c3f56bf4c4a6e4c54282ae7a1af89b9d2a8b2241c3f56bf4c4origin/merge_cia6e4c54282ae7a1af89b9d2a8b2241c3f56bf4c4a6e4c54282ae7a1af89b9d2a8b2241c3f56bf4c4origin/merge_cia6e4c54282ae7a1af89b9d2a8b2241c3f56bf4c4a6e4c54282ae7a1af89b9d2a8b2241c3f56bf4c4origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#139129199128153BIOFORMATS-build » testintegration #139139falsefalse1395412SUCCESS1776384324048https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/139/testintegration32b2e8e104b5c3d81b9de820a58594a23ad0826e1776384023000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#143 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/143/) 2026-04-17 00:00:23 +000032b2e8e104b5c3d81b9de820a58594a23ad0826emerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit9a34c41d889bfdf8fe17d87769d2e8bbfdd0fce21776384214000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#143 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/143/) 2026-04-17 00:03:34 +00009a34c41d889bfdf8fe17d87769d2e8bbfdd0fce2merge master -Dorg -Ssuccess-onlyeditome-stubseditbio-formats-documentationeditZarrReadereditome-common-javaeditome-metakiteditome-mdbtoolseditome-jaieditome-codecseditbioformatseditome-poieditbio-formats-exampleseditome-modeledit.gitmodulesbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakita6e4c54282ae7a1af89b9d2a8b2241c3f56bf4c41776384313000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-17 00:05:13 +0000a6e4c54282ae7a1af89b9d2a8b2241c3f56bf4c4Update component versionseditome-modeleditome-codecseditome-metakiteditbio-formats-documentationeditbio-formats-exampleseditbioformatseditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 138138BIOFORMATS-buildjob/BIOFORMATS-build/138da3c533d65dfb76be3fc1a36749af3ede7090d09da3c533d65dfb76be3fc1a36749af3ede7090d09origin/merge_cida3c533d65dfb76be3fc1a36749af3ede7090d09da3c533d65dfb76be3fc1a36749af3ede7090d09origin/merge_cida3c533d65dfb76be3fc1a36749af3ede7090d09da3c533d65dfb76be3fc1a36749af3ede7090d09origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#138127624128153BIOFORMATS-build » testintegration #138138falsefalse1385387SUCCESS1776354958290https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/138/testintegration3f283a42ca44fc5e02a26885125dd05fc278a02a1776354646000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#142 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/142/) 2026-04-16 15:50:46 +00003f283a42ca44fc5e02a26885125dd05fc278a02amerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit692651ff354b20f84915ba5f8fe1a050ca11f07e1776354845000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#142 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/142/) 2026-04-16 15:54:05 +0000692651ff354b20f84915ba5f8fe1a050ca11f07emerge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditZarrReadereditome-stubseditome-poieditome-modeleditome-jaieditome-mdbtoolseditome-metakitedit.gitmoduleseditbio-formats-documentationeditome-codecseditbioformatseditome-common-javabioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitda3c533d65dfb76be3fc1a36749af3ede7090d091776354950000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-16 15:55:50 +0000da3c533d65dfb76be3fc1a36749af3ede7090d09Update component versionseditbioformatseditome-modeleditome-poieditbio-formats-exampleseditome-codecseditome-metakiteditbio-formats-documentationgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 137137BIOFORMATS-buildjob/BIOFORMATS-build/1375b486a72be3f3543c5934be98f7e3bd95d0ef79b5b486a72be3f3543c5934be98f7e3bd95d0ef79borigin/merge_ci5b486a72be3f3543c5934be98f7e3bd95d0ef79b5b486a72be3f3543c5934be98f7e3bd95d0ef79borigin/merge_ci5b486a72be3f3543c5934be98f7e3bd95d0ef79b5b486a72be3f3543c5934be98f7e3bd95d0ef79borigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#137132599128153BIOFORMATS-build » testintegration #137137falsefalse1375364SUCCESS1776352048204https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/137/testintegrationf212ce7db9830b65ee4a7ba59dad6d19c8030f5e1776351732000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#141 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/141/) 2026-04-16 15:02:12 +0000f212ce7db9830b65ee4a7ba59dad6d19c8030f5emerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit6bf2f1d2a7512bb0391c556d70e471257d13441b1776351936000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#141 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/141/) 2026-04-16 15:05:36 +00006bf2f1d2a7512bb0391c556d70e471257d13441bmerge master -Dorg -Ssuccess-onlyeditome-jaieditbio-formats-examplesedit.gitmoduleseditome-metakiteditZarrReadereditome-stubseditome-codecseditome-poieditome-modeleditbio-formats-documentationeditome-mdbtoolseditbioformatseditome-common-javabioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit5b486a72be3f3543c5934be98f7e3bd95d0ef79b1776352037000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-16 15:07:17 +00005b486a72be3f3543c5934be98f7e3bd95d0ef79bUpdate component versionseditome-metakiteditome-modeleditome-codecseditbio-formats-documentationeditbio-formats-exampleseditome-poieditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 136136BIOFORMATS-buildjob/BIOFORMATS-build/136fff8e3217fb47a6a5a128e4fd2af847ed3db13bdfff8e3217fb47a6a5a128e4fd2af847ed3db13bdorigin/merge_cifff8e3217fb47a6a5a128e4fd2af847ed3db13bdfff8e3217fb47a6a5a128e4fd2af847ed3db13bdorigin/merge_cifff8e3217fb47a6a5a128e4fd2af847ed3db13bdfff8e3217fb47a6a5a128e4fd2af847ed3db13bdorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#136142856128153BIOFORMATS-build » testintegration #136136falsefalse1365339SUCCESS1776344167991https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/136/testintegrationb4838eb7b6cdb4a3ca11b415d94ad802c7b297771776343851000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#140 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/140/) 2026-04-16 12:50:51 +0000b4838eb7b6cdb4a3ca11b415d94ad802c7b29777merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakita69fe19d97ab6645f56054be65dcf9f826cf82b11776344059000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#140 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/140/) 2026-04-16 12:54:19 +0000a69fe19d97ab6645f56054be65dcf9f826cf82b1merge master -Dorg -Ssuccess-onlyeditZarrReadereditome-common-javaeditome-poieditome-codecsedit.gitmoduleseditbioformatseditome-metakiteditome-stubseditome-modeleditome-jaieditome-mdbtoolseditbio-formats-exampleseditbio-formats-documentationbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitfff8e3217fb47a6a5a128e4fd2af847ed3db13bd1776344157000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-16 12:55:57 +0000fff8e3217fb47a6a5a128e4fd2af847ed3db13bdUpdate component versionseditbio-formats-documentationeditbio-formats-exampleseditome-metakiteditbioformatseditome-modeleditome-codecseditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 135135BIOFORMATS-buildjob/BIOFORMATS-build/1352e1ea95ef509078cd7546008ab395b44e1c456572e1ea95ef509078cd7546008ab395b44e1c45657origin/merge_ci2e1ea95ef509078cd7546008ab395b44e1c456572e1ea95ef509078cd7546008ab395b44e1c45657origin/merge_ci2e1ea95ef509078cd7546008ab395b44e1c456572e1ea95ef509078cd7546008ab395b44e1c45657origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#135134000128153BIOFORMATS-build » testintegration #135135falsefalse1355326SUCCESS1776342637942https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/135/testintegration809f00a37b496cf746217d71d6850fafc72c70e51776342322000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#139 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/139/) 2026-04-16 12:25:22 +0000809f00a37b496cf746217d71d6850fafc72c70e5merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakita73e5e49515ddb1535d510da7b2465dca209832b1776342526000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#139 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/139/) 2026-04-16 12:28:46 +0000a73e5e49515ddb1535d510da7b2465dca209832bmerge master -Dorg -Ssuccess-onlyeditome-poiedit.gitmoduleseditome-common-javaeditbio-formats-exampleseditbioformatseditome-jaieditome-modeleditome-mdbtoolseditZarrReadereditome-codecseditome-stubseditome-metakiteditbio-formats-documentationbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit2e1ea95ef509078cd7546008ab395b44e1c456571776342626000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-16 12:30:26 +00002e1ea95ef509078cd7546008ab395b44e1c45657Update component versionseditbioformatseditbio-formats-exampleseditome-metakiteditbio-formats-documentationeditome-modeleditome-codecseditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 134134BIOFORMATS-buildjob/BIOFORMATS-build/134c54f94afc8c81f6e7219b5cf47e8a3a05fddb9dcc54f94afc8c81f6e7219b5cf47e8a3a05fddb9dcorigin/merge_cic54f94afc8c81f6e7219b5cf47e8a3a05fddb9dcc54f94afc8c81f6e7219b5cf47e8a3a05fddb9dcorigin/merge_cic54f94afc8c81f6e7219b5cf47e8a3a05fddb9dcc54f94afc8c81f6e7219b5cf47e8a3a05fddb9dcorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#134129433128153BIOFORMATS-build » testintegration #134134falsefalse1345269SUCCESS1776297921769https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/134/testintegration2e5edaa342841ab4b9bf43f34bcd41806626c61d1776297621000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#138 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/138/) 2026-04-16 00:00:21 +00002e5edaa342841ab4b9bf43f34bcd41806626c61dmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit532bb2be4021a946f3cc46019d36509fd1785e161776297812000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#138 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/138/) 2026-04-16 00:03:32 +0000532bb2be4021a946f3cc46019d36509fd1785e16merge master -Dorg -Ssuccess-onlyeditome-metakiteditome-jaieditZarrReadereditome-stubseditbio-formats-exampleseditome-mdbtoolsedit.gitmoduleseditome-codecseditome-common-javaeditome-poieditbio-formats-documentationeditome-modeleditbioformatsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitc54f94afc8c81f6e7219b5cf47e8a3a05fddb9dc1776297912000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-16 00:05:12 +0000c54f94afc8c81f6e7219b5cf47e8a3a05fddb9dcUpdate component versionseditome-codecseditbio-formats-documentationeditbioformatseditome-metakiteditome-modeleditome-poieditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 133133BIOFORMATS-buildjob/BIOFORMATS-build/1335e5e032e66d22237f12e80e813aa34831edd1e445e5e032e66d22237f12e80e813aa34831edd1e44origin/merge_ci5e5e032e66d22237f12e80e813aa34831edd1e445e5e032e66d22237f12e80e813aa34831edd1e44origin/merge_ci5e5e032e66d22237f12e80e813aa34831edd1e445e5e032e66d22237f12e80e813aa34831edd1e44origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#133134414128153BIOFORMATS-build » testintegration #133133falsefalse1335225SUCCESS1776260680816https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/133/testintegration6daf19da14accec7eb118342266cce421dc25afb1776260369000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#137 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/137/) 2026-04-15 13:39:29 +00006daf19da14accec7eb118342266cce421dc25afbmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit1cf7a2efcb02a95e4142f83b1226c73ca54c48a71776260570000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#137 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/137/) 2026-04-15 13:42:50 +00001cf7a2efcb02a95e4142f83b1226c73ca54c48a7merge master -Dorg -Ssuccess-onlyeditome-mdbtoolseditome-codecseditZarrReadereditome-jaieditome-modeleditome-metakiteditbio-formats-exampleseditbio-formats-documentationeditome-common-javaeditbioformatsedit.gitmoduleseditome-stubseditome-poibioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit5e5e032e66d22237f12e80e813aa34831edd1e441776260670000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-15 13:44:30 +00005e5e032e66d22237f12e80e813aa34831edd1e44Update component versionseditbio-formats-documentationeditbioformatseditome-codecseditome-metakiteditome-poieditome-modeleditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 132132BIOFORMATS-buildjob/BIOFORMATS-build/132ff5a0ef8c84a39c8fc403de70ee81ad2f254e02bff5a0ef8c84a39c8fc403de70ee81ad2f254e02borigin/merge_ciff5a0ef8c84a39c8fc403de70ee81ad2f254e02bff5a0ef8c84a39c8fc403de70ee81ad2f254e02borigin/merge_ciff5a0ef8c84a39c8fc403de70ee81ad2f254e02bff5a0ef8c84a39c8fc403de70ee81ad2f254e02borigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#132136083128153BIOFORMATS-build » testintegration #132132falsefalse1325201SUCCESS1776249895525https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/132/testintegration4b6331a365d1f43902177a2092d9af4d1ce4ef141776249594000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#136 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/136/) 2026-04-15 10:39:54 +00004b6331a365d1f43902177a2092d9af4d1ce4ef14merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit079124da5447b42e8855b6212d703d68aca0b6081776249786000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#136 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/136/) 2026-04-15 10:43:06 +0000079124da5447b42e8855b6212d703d68aca0b608merge master -Dorg -Ssuccess-onlyedit.gitmoduleseditome-common-javaeditome-metakiteditome-modeleditome-stubseditZarrReadereditbio-formats-documentationeditbioformatseditbio-formats-exampleseditome-poieditome-codecseditome-jaieditome-mdbtoolsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitff5a0ef8c84a39c8fc403de70ee81ad2f254e02b1776249884000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-15 10:44:44 +0000ff5a0ef8c84a39c8fc403de70ee81ad2f254e02bUpdate component versionseditome-metakiteditome-modeleditbio-formats-exampleseditbio-formats-documentationeditome-codecseditbioformatseditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 131131BIOFORMATS-buildjob/BIOFORMATS-build/131bac9307fc98e7fead352e45cd27eaa53dbe666ffbac9307fc98e7fead352e45cd27eaa53dbe666fforigin/merge_cibac9307fc98e7fead352e45cd27eaa53dbe666ffbac9307fc98e7fead352e45cd27eaa53dbe666fforigin/merge_cibac9307fc98e7fead352e45cd27eaa53dbe666ffbac9307fc98e7fead352e45cd27eaa53dbe666fforigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#131136545128153BIOFORMATS-build » testintegration #131131falsefalse1315177SUCCESS1776245825397https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/131/testintegrationaa8f7c2634c2c7074ff1ef3a685cd0c724f3bba21776245519000https://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#135 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/135/) 2026-04-15 09:31:59 +0000aa8f7c2634c2c7074ff1ef3a685cd0c724f3bba2merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitcc3a33825cd19749054788b7197e5aeb34d6f2fd1776245717000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#135 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/135/) 2026-04-15 09:35:17 +0000cc3a33825cd19749054788b7197e5aeb34d6f2fdmerge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditome-stubseditome-poieditome-mdbtoolseditome-common-javaeditome-metakiteditZarrReadereditbioformatseditome-codecseditome-modeleditbio-formats-documentationeditome-jaiedit.gitmodulesbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitbac9307fc98e7fead352e45cd27eaa53dbe666ff1776245816000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-15 09:36:56 +0000bac9307fc98e7fead352e45cd27eaa53dbe666ffUpdate component versionseditbioformatseditome-metakiteditome-modeleditome-codecseditome-poieditbio-formats-documentationeditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 130130BIOFORMATS-buildjob/BIOFORMATS-build/1302c01269069ac75dc94991ee66596a3e11b89120b2c01269069ac75dc94991ee66596a3e11b89120borigin/merge_ci2c01269069ac75dc94991ee66596a3e11b89120b2c01269069ac75dc94991ee66596a3e11b89120borigin/merge_ci2c01269069ac75dc94991ee66596a3e11b89120b2c01269069ac75dc94991ee66596a3e11b89120borigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#130236260128153BIOFORMATS-build » testintegration #130130falsefalse1305133SUCCESS1776211574440https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/130/testintegration212b075d8da569d18ced2ffc708999c8e076bfa71776211264000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#134 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/134/) 2026-04-15 00:01:04 +0000212b075d8da569d18ced2ffc708999c8e076bfa7merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakite1b7a7af1de31905b8a0e44c07aa5b842b201d221776211453000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#134 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/134/) 2026-04-15 00:04:13 +0000e1b7a7af1de31905b8a0e44c07aa5b842b201d22merge master -Dorg -Ssuccess-onlyeditome-codecsedit.gitmoduleseditome-jaieditbio-formats-exampleseditbio-formats-documentationeditome-poieditome-mdbtoolseditome-metakiteditome-common-javaeditome-modeleditZarrReadereditbioformatseditome-stubsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit2c01269069ac75dc94991ee66596a3e11b89120b1776211562000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-15 00:06:02 +00002c01269069ac75dc94991ee66596a3e11b89120bUpdate component versionseditbio-formats-documentationeditbio-formats-exampleseditbioformatseditome-codecseditome-metakiteditome-modeleditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 129129BIOFORMATS-buildjob/BIOFORMATS-build/1296dfe0ca8fc90940c92441f7679968c11a1d7cbd66dfe0ca8fc90940c92441f7679968c11a1d7cbd6origin/merge_ci6dfe0ca8fc90940c92441f7679968c11a1d7cbd66dfe0ca8fc90940c92441f7679968c11a1d7cbd6origin/merge_ci6dfe0ca8fc90940c92441f7679968c11a1d7cbd66dfe0ca8fc90940c92441f7679968c11a1d7cbd6origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#129127951128153BIOFORMATS-build » testintegration #129129falsefalse1295092SUCCESS1776181873616https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/129/testintegrationc6b22b0d7209646dc8e828ac7288f76ce7b0227c1776181563000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#133 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/133/) 2026-04-14 15:46:03 +0000c6b22b0d7209646dc8e828ac7288f76ce7b0227cmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitc11195d052861b7657bd9212ff8870225b46abdc1776181764000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#133 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/133/) 2026-04-14 15:49:24 +0000c11195d052861b7657bd9212ff8870225b46abdcmerge master -Dorg -Ssuccess-onlyeditome-poieditZarrReadereditome-metakiteditbio-formats-documentationeditome-mdbtoolsedit.gitmoduleseditbioformatseditome-jaieditome-modeleditome-stubseditbio-formats-exampleseditome-common-javaeditome-codecsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit6dfe0ca8fc90940c92441f7679968c11a1d7cbd61776181864000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-14 15:51:04 +00006dfe0ca8fc90940c92441f7679968c11a1d7cbd6Update component versionseditome-codecseditbioformatseditome-poieditbio-formats-documentationeditome-metakiteditbio-formats-exampleseditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 128128BIOFORMATS-buildjob/BIOFORMATS-build/12851852e135226653c601bbd4bcf0ceaa088b1f08751852e135226653c601bbd4bcf0ceaa088b1f087origin/merge_ci51852e135226653c601bbd4bcf0ceaa088b1f08751852e135226653c601bbd4bcf0ceaa088b1f087origin/merge_ci51852e135226653c601bbd4bcf0ceaa088b1f08751852e135226653c601bbd4bcf0ceaa088b1f087origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#128130455128153BIOFORMATS-build » testintegration #128128falsefalse1285068SUCCESS1776175843463https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/128/testintegrationabf2816835b6cbd7610dce59c354e4d723061a7f1776175522000https://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#132 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/132/) 2026-04-14 14:05:22 +0000abf2816835b6cbd7610dce59c354e4d723061a7fmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakita30906be67c7de89873ce9a8d0e6217ba22f48d61776175731000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#132 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/132/) 2026-04-14 14:08:51 +0000a30906be67c7de89873ce9a8d0e6217ba22f48d6merge master -Dorg -Ssuccess-onlyeditZarrReadereditome-poieditome-jaieditome-stubseditome-metakiteditome-modeleditbio-formats-examplesedit.gitmoduleseditome-common-javaeditbio-formats-documentationeditome-mdbtoolseditome-codecseditbioformatsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit51852e135226653c601bbd4bcf0ceaa088b1f0871776175832000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-14 14:10:32 +000051852e135226653c601bbd4bcf0ceaa088b1f087Update component versionseditome-modeleditome-metakiteditome-poieditbio-formats-documentationeditbio-formats-exampleseditbioformatseditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 127127BIOFORMATS-buildjob/BIOFORMATS-build/127c201a2a3816fd8bc23ef7c4aababb666b6cb5844c201a2a3816fd8bc23ef7c4aababb666b6cb5844origin/merge_cic201a2a3816fd8bc23ef7c4aababb666b6cb5844c201a2a3816fd8bc23ef7c4aababb666b6cb5844origin/merge_cic201a2a3816fd8bc23ef7c4aababb666b6cb5844c201a2a3816fd8bc23ef7c4aababb666b6cb5844origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#127127232128153BIOFORMATS-build » testintegration #127127falsefalse1275034SUCCESS1776165283196https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/127/testintegrationfcf3fc2b11bf4e8d5ffc1edf4c11b51f8b321f381776164981000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#131 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/131/) 2026-04-14 11:09:41 +0000fcf3fc2b11bf4e8d5ffc1edf4c11b51f8b321f38merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitb941e47cb4fddca4b35080216136b63390fcf8461776165175000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#131 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/131/) 2026-04-14 11:12:55 +0000b941e47cb4fddca4b35080216136b63390fcf846merge master -Dorg -Ssuccess-onlyeditZarrReadereditome-modeleditome-jaieditome-stubseditbio-formats-documentationeditome-codecseditome-mdbtoolseditome-common-javaeditome-poiedit.gitmoduleseditbio-formats-exampleseditome-metakiteditbioformatsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitc201a2a3816fd8bc23ef7c4aababb666b6cb58441776165274000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-14 11:14:34 +0000c201a2a3816fd8bc23ef7c4aababb666b6cb5844Update component versionseditome-poieditome-codecseditbio-formats-exampleseditbioformatseditbio-formats-documentationeditome-metakiteditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 126126BIOFORMATS-buildjob/BIOFORMATS-build/126d4acebf574fc25762d12ee505426fdf47e484ebbd4acebf574fc25762d12ee505426fdf47e484ebborigin/merge_cid4acebf574fc25762d12ee505426fdf47e484ebbd4acebf574fc25762d12ee505426fdf47e484ebborigin/merge_cid4acebf574fc25762d12ee505426fdf47e484ebbd4acebf574fc25762d12ee505426fdf47e484ebborigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#126129028128153BIOFORMATS-build » testintegration #126126falsefalse1265019SUCCESS1776163548146https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/126/testintegrationa655d517d63d486386f0d7b47f82bbf3c40fe18e1776163246000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#130 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/130/) 2026-04-14 10:40:46 +0000a655d517d63d486386f0d7b47f82bbf3c40fe18emerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitdba1e3b2884f9060066d8ad13e0f89c654faa0c31776163440000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#130 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/130/) 2026-04-14 10:44:00 +0000dba1e3b2884f9060066d8ad13e0f89c654faa0c3merge master -Dorg -Ssuccess-onlyedit.gitmoduleseditome-common-javaeditome-mdbtoolseditome-jaieditbio-formats-exampleseditome-codecseditome-metakiteditome-modeleditbioformatseditome-poieditZarrReadereditbio-formats-documentationeditome-stubsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitd4acebf574fc25762d12ee505426fdf47e484ebb1776163540000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-14 10:45:40 +0000d4acebf574fc25762d12ee505426fdf47e484ebbUpdate component versionseditbio-formats-documentationeditome-codecseditome-modeleditome-poieditome-metakiteditbioformatseditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 125125BIOFORMATS-buildjob/BIOFORMATS-build/125f26549a09785e9a3297c05903919ea0eb26246f3f26549a09785e9a3297c05903919ea0eb26246f3origin/merge_cif26549a09785e9a3297c05903919ea0eb26246f3f26549a09785e9a3297c05903919ea0eb26246f3origin/merge_cif26549a09785e9a3297c05903919ea0eb26246f3f26549a09785e9a3297c05903919ea0eb26246f3origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#125132040128153BIOFORMATS-build » testintegration #125125falsefalse1254973SUCCESS1776125117235https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/125/testintegrationd2cff407aa8eb31fe446c74e0bb05e9366665db81776124822000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#129 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/129/) 2026-04-14 00:00:22 +0000d2cff407aa8eb31fe446c74e0bb05e9366665db8merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit131823246ef7a39d5cf267c12739d2b01a54f1d41776125007000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#129 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/129/) 2026-04-14 00:03:27 +0000131823246ef7a39d5cf267c12739d2b01a54f1d4merge master -Dorg -Ssuccess-onlyeditome-poieditome-metakiteditome-stubseditbio-formats-exampleseditome-common-javaeditome-jaieditome-mdbtoolseditbio-formats-documentationedit.gitmoduleseditZarrReadereditome-codecseditbioformatseditome-modelbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitf26549a09785e9a3297c05903919ea0eb26246f31776125106000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-14 00:05:06 +0000f26549a09785e9a3297c05903919ea0eb26246f3Update component versionseditbio-formats-exampleseditome-modeleditbio-formats-documentationeditome-metakiteditome-codecseditbioformatseditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 124124BIOFORMATS-buildjob/BIOFORMATS-build/12424c49cada863af5f9a00c1558e63548494c1f6fa24c49cada863af5f9a00c1558e63548494c1f6faorigin/merge_ci24c49cada863af5f9a00c1558e63548494c1f6fa24c49cada863af5f9a00c1558e63548494c1f6faorigin/merge_ci24c49cada863af5f9a00c1558e63548494c1f6fa24c49cada863af5f9a00c1558e63548494c1f6faorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#124128690128153BIOFORMATS-build » testintegration #124124falsefalse1244914SUCCESS1776038720152https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/124/testintegratione011169d757861b2cfbd412c2599d65bba0febca1776038424000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#128 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/128/) 2026-04-13 00:00:24 +0000e011169d757861b2cfbd412c2599d65bba0febcamerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit3f65846ff780141ba3d11074859bd8ed22453bf81776038611000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#128 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/128/) 2026-04-13 00:03:31 +00003f65846ff780141ba3d11074859bd8ed22453bf8merge master -Dorg -Ssuccess-onlyeditome-stubseditbio-formats-documentationeditZarrReadereditome-metakiteditome-common-javaeditome-jaiedit.gitmoduleseditbio-formats-exampleseditome-mdbtoolseditbioformatseditome-poieditome-codecseditome-modelbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit24c49cada863af5f9a00c1558e63548494c1f6fa1776038709000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-13 00:05:09 +000024c49cada863af5f9a00c1558e63548494c1f6faUpdate component versionseditome-codecseditome-modeleditome-metakiteditbio-formats-exampleseditome-poieditbioformatseditbio-formats-documentationgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 123123BIOFORMATS-buildjob/BIOFORMATS-build/123a7a2b55e612c97056cea380c535b32f69a41f195a7a2b55e612c97056cea380c535b32f69a41f195origin/merge_cia7a2b55e612c97056cea380c535b32f69a41f195a7a2b55e612c97056cea380c535b32f69a41f195origin/merge_cia7a2b55e612c97056cea380c535b32f69a41f195a7a2b55e612c97056cea380c535b32f69a41f195origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#123131664128153BIOFORMATS-build » testintegration #123123falsefalse1234873SUCCESS1775952318047https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/123/testintegration6b435801c8560e3de2ee1c610511b542a47fd9ef1775952021000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#127 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/127/) 2026-04-12 00:00:21 +00006b435801c8560e3de2ee1c610511b542a47fd9efmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit1806b625b39eadd716272417b7bd40be113d5c201775952208000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#127 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/127/) 2026-04-12 00:03:28 +00001806b625b39eadd716272417b7bd40be113d5c20merge master -Dorg -Ssuccess-onlyeditome-metakiteditbio-formats-exampleseditome-codecseditome-stubseditZarrReadereditbioformatseditome-poieditome-jaieditbio-formats-documentationeditome-mdbtoolseditome-common-javaedit.gitmoduleseditome-modelbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakita7a2b55e612c97056cea380c535b32f69a41f1951775952307000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-12 00:05:07 +0000a7a2b55e612c97056cea380c535b32f69a41f195Update component versionseditome-modeleditbio-formats-exampleseditome-poieditome-metakiteditbio-formats-documentationeditbioformatseditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 122122BIOFORMATS-buildjob/BIOFORMATS-build/1223c52f77fe5ac234dcfc07511e6f8c6201094fa5a3c52f77fe5ac234dcfc07511e6f8c6201094fa5aorigin/merge_ci3c52f77fe5ac234dcfc07511e6f8c6201094fa5a3c52f77fe5ac234dcfc07511e6f8c6201094fa5aorigin/merge_ci3c52f77fe5ac234dcfc07511e6f8c6201094fa5a3c52f77fe5ac234dcfc07511e6f8c6201094fa5aorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#122135308128153BIOFORMATS-build » testintegration #122122falsefalse1224832SUCCESS1775865915920https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/122/testintegrationa739718b2f7760f40f5c07130a23ec0d9f34d3291775865624000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#126 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/126/) 2026-04-11 00:00:24 +0000a739718b2f7760f40f5c07130a23ec0d9f34d329merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit0b09098649c96e0eefe337cd6718ab4630943ab21775865809000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#126 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/126/) 2026-04-11 00:03:29 +00000b09098649c96e0eefe337cd6718ab4630943ab2merge master -Dorg -Ssuccess-onlyeditome-stubseditbio-formats-exampleseditome-codecseditome-modeleditZarrReadereditbioformatseditome-poieditbio-formats-documentationedit.gitmoduleseditome-metakiteditome-mdbtoolseditome-jaieditome-common-javabioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit3c52f77fe5ac234dcfc07511e6f8c6201094fa5a1775865908000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-11 00:05:08 +00003c52f77fe5ac234dcfc07511e6f8c6201094fa5aUpdate component versionseditbio-formats-documentationeditome-codecseditbioformatseditome-metakiteditbio-formats-exampleseditome-poieditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 121121BIOFORMATS-buildjob/BIOFORMATS-build/121f2dd8d727fb8e1e719475e267bb8d79a37aaa77ef2dd8d727fb8e1e719475e267bb8d79a37aaa77eorigin/merge_cif2dd8d727fb8e1e719475e267bb8d79a37aaa77ef2dd8d727fb8e1e719475e267bb8d79a37aaa77eorigin/merge_cif2dd8d727fb8e1e719475e267bb8d79a37aaa77ef2dd8d727fb8e1e719475e267bb8d79a37aaa77eorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#121141507128153BIOFORMATS-build » testintegration #121121falsefalse1214791SUCCESS1775779523763https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/121/testintegration12a2576659fdc11df617bcde33910f8ffd651bec1775779225000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#125 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/125/) 2026-04-10 00:00:25 +000012a2576659fdc11df617bcde33910f8ffd651becmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit62d9c1515c2cad4fe440b1664c6bcb8b44c22c9a1775779415000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#125 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/125/) 2026-04-10 00:03:35 +000062d9c1515c2cad4fe440b1664c6bcb8b44c22c9amerge master -Dorg -Ssuccess-onlyeditome-poieditome-jaieditbio-formats-exampleseditome-stubsedit.gitmoduleseditome-modeleditZarrReadereditbioformatseditome-common-javaeditome-mdbtoolseditome-codecseditome-metakiteditbio-formats-documentationbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitf2dd8d727fb8e1e719475e267bb8d79a37aaa77e1775779514000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-10 00:05:14 +0000f2dd8d727fb8e1e719475e267bb8d79a37aaa77eUpdate component versionseditbioformatseditome-codecseditbio-formats-documentationeditbio-formats-exampleseditome-metakiteditome-modeleditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 120120BIOFORMATS-buildjob/BIOFORMATS-build/1209503a6310526930daed269a88f2a3b33ca622cc49503a6310526930daed269a88f2a3b33ca622cc4origin/merge_ci9503a6310526930daed269a88f2a3b33ca622cc49503a6310526930daed269a88f2a3b33ca622cc4origin/merge_ci9503a6310526930daed269a88f2a3b33ca622cc49503a6310526930daed269a88f2a3b33ca622cc4origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#120138001128153BIOFORMATS-build » testintegration #120120falsefalse1204749SUCCESS1775693122611https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/120/testintegration52ade4b0fba45b6abc3ea282796ffdc00dc780be1775692821000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#124 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/124/) 2026-04-09 00:00:21 +000052ade4b0fba45b6abc3ea282796ffdc00dc780bemerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit50fafe24de1d0ad46a11686e0aa084392c8f24a51775693011000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#124 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/124/) 2026-04-09 00:03:31 +000050fafe24de1d0ad46a11686e0aa084392c8f24a5merge master -Dorg -Ssuccess-onlyeditome-common-javaeditZarrReadereditbio-formats-documentationeditome-mdbtoolseditome-codecseditbio-formats-exampleseditbioformatsedit.gitmoduleseditome-modeleditome-stubseditome-poieditome-jaieditome-metakitbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit9503a6310526930daed269a88f2a3b33ca622cc41775693111000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-09 00:05:11 +00009503a6310526930daed269a88f2a3b33ca622cc4Update component versionseditbioformatseditome-poieditome-codecseditbio-formats-documentationeditome-modeleditbio-formats-exampleseditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 119119BIOFORMATS-buildjob/BIOFORMATS-build/119797b2ad9441820f19021cdd176d09822174c2620797b2ad9441820f19021cdd176d09822174c2620origin/merge_ci797b2ad9441820f19021cdd176d09822174c2620797b2ad9441820f19021cdd176d09822174c2620origin/merge_ci797b2ad9441820f19021cdd176d09822174c2620797b2ad9441820f19021cdd176d09822174c2620origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#119239594128153BIOFORMATS-build » testintegration #119119falsefalse1194724SUCCESS1775641251254https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/119/testintegration22b388f4137cc6ec6e86a95cd87d98dc14692a6e1775640928000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#123 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/123/) 2026-04-08 09:35:28 +000022b388f4137cc6ec6e86a95cd87d98dc14692a6emerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit255153215e7a361472259fb185a1c857d5799e181775641128000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#123 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/123/) 2026-04-08 09:38:48 +0000255153215e7a361472259fb185a1c857d5799e18merge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditZarrReadereditome-modeleditome-mdbtoolseditome-stubseditome-metakiteditome-jaieditbio-formats-documentationedit.gitmoduleseditbioformatseditome-common-javaeditome-codecseditome-poibioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit797b2ad9441820f19021cdd176d09822174c26201775641240000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-08 09:40:40 +0000797b2ad9441820f19021cdd176d09822174c2620Update component versionseditome-codecseditbioformatseditome-modeleditome-metakiteditbio-formats-documentationeditbio-formats-exampleseditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 118118BIOFORMATS-buildjob/BIOFORMATS-build/1185d307b5fcb2dcd1e0fcfefaed4bff5c8e4637bd75d307b5fcb2dcd1e0fcfefaed4bff5c8e4637bd7origin/merge_ci5d307b5fcb2dcd1e0fcfefaed4bff5c8e4637bd75d307b5fcb2dcd1e0fcfefaed4bff5c8e4637bd7origin/merge_ci5d307b5fcb2dcd1e0fcfefaed4bff5c8e4637bd75d307b5fcb2dcd1e0fcfefaed4bff5c8e4637bd7origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#118131369128153BIOFORMATS-build » testintegration #118118falsefalse1184679SUCCESS1775520321179https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/118/testintegration7d02b97079ac9c7787422ccc2422ec0e0d97dbcc1775520020000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#122 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/122/) 2026-04-07 00:00:20 +00007d02b97079ac9c7787422ccc2422ec0e0d97dbccmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitb2c28126156200ebb339b991ab4cf3094ec160001775520209000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#122 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/122/) 2026-04-07 00:03:29 +0000b2c28126156200ebb339b991ab4cf3094ec16000merge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditome-mdbtoolseditZarrReadereditome-common-javaeditome-poieditome-metakiteditome-modeleditbioformatseditome-codecsedit.gitmoduleseditome-stubseditbio-formats-documentationeditome-jaibioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit5d307b5fcb2dcd1e0fcfefaed4bff5c8e4637bd71775520309000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-07 00:05:09 +00005d307b5fcb2dcd1e0fcfefaed4bff5c8e4637bd7Update component versionseditome-metakiteditbioformatseditome-poieditbio-formats-exampleseditome-codecseditbio-formats-documentationeditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 117117BIOFORMATS-buildjob/BIOFORMATS-build/117d88a63928e6aaac86147c94564addc7cd9e84aeed88a63928e6aaac86147c94564addc7cd9e84aeeorigin/merge_cid88a63928e6aaac86147c94564addc7cd9e84aeed88a63928e6aaac86147c94564addc7cd9e84aeeorigin/merge_cid88a63928e6aaac86147c94564addc7cd9e84aeed88a63928e6aaac86147c94564addc7cd9e84aeeorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#117126636128153BIOFORMATS-build » testintegration #117117falsefalse1174638SUCCESS1775433919108https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/117/testintegrationccf742da6676c46c7f4437a8b4e07e277396574a1775433624000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#121 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/121/) 2026-04-06 00:00:24 +0000ccf742da6676c46c7f4437a8b4e07e277396574amerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitbf60fef9bbdbb9901fb45ac0fe0c3625058764f61775433812000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#121 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/121/) 2026-04-06 00:03:32 +0000bf60fef9bbdbb9901fb45ac0fe0c3625058764f6merge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditome-modeleditZarrReadereditome-common-javaeditbioformatseditome-jaieditome-metakiteditbio-formats-exampleseditome-stubsedit.gitmoduleseditome-mdbtoolseditome-codecseditome-poibioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitd88a63928e6aaac86147c94564addc7cd9e84aee1775433908000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-06 00:05:08 +0000d88a63928e6aaac86147c94564addc7cd9e84aeeUpdate component versionseditome-codecseditome-modeleditbioformatseditbio-formats-documentationeditome-poieditome-metakiteditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 116116BIOFORMATS-buildjob/BIOFORMATS-build/116622ca8141aa4a8935dcab14bd448d9849b00aace622ca8141aa4a8935dcab14bd448d9849b00aaceorigin/merge_ci622ca8141aa4a8935dcab14bd448d9849b00aace622ca8141aa4a8935dcab14bd448d9849b00aaceorigin/merge_ci622ca8141aa4a8935dcab14bd448d9849b00aace622ca8141aa4a8935dcab14bd448d9849b00aaceorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#116127822128153BIOFORMATS-build » testintegration #116116falsefalse1164597SUCCESS1775347516992https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/116/testintegration18dc0e5a291ecdcb2a6ddeb20571b1bc7cbaccad1775347221000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#120 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/120/) 2026-04-05 00:00:21 +000018dc0e5a291ecdcb2a6ddeb20571b1bc7cbaccadmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit7b09260abdcd792f28245f91a08a959f68e447661775347407000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#120 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/120/) 2026-04-05 00:03:27 +00007b09260abdcd792f28245f91a08a959f68e44766merge master -Dorg -Ssuccess-onlyeditome-stubseditbio-formats-exampleseditome-jaieditbioformatseditbio-formats-documentationeditome-metakiteditome-common-javaeditome-modeledit.gitmoduleseditome-mdbtoolseditZarrReadereditome-codecseditome-poibioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit622ca8141aa4a8935dcab14bd448d9849b00aace1775347505000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-05 00:05:05 +0000622ca8141aa4a8935dcab14bd448d9849b00aaceUpdate component versionseditome-metakiteditome-modeleditbio-formats-exampleseditbioformatseditbio-formats-documentationeditome-codecseditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 115115BIOFORMATS-buildjob/BIOFORMATS-build/1159b0d2b4d9eb8827f1931b572478ad7b1f39a78399b0d2b4d9eb8827f1931b572478ad7b1f39a7839origin/merge_ci9b0d2b4d9eb8827f1931b572478ad7b1f39a78399b0d2b4d9eb8827f1931b572478ad7b1f39a7839origin/merge_ci9b0d2b4d9eb8827f1931b572478ad7b1f39a78399b0d2b4d9eb8827f1931b572478ad7b1f39a7839origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#115127789128153BIOFORMATS-build » testintegration #115115falsefalse1154556SUCCESS1775294600664https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/115/testintegrationc4d96a966b8df7dce828e52f6b0dbbf964ac033c1775294313000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#119 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/119/) 2026-04-04 09:18:33 +0000c4d96a966b8df7dce828e52f6b0dbbf964ac033cmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit712da5e59cfcf9ba2722fac0cc50414a842486e91775294496000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#119 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/119/) 2026-04-04 09:21:36 +0000712da5e59cfcf9ba2722fac0cc50414a842486e9merge master -Dorg -Ssuccess-onlyeditome-modeleditome-codecseditome-jaieditome-poieditome-metakiteditbio-formats-documentationeditZarrReadereditome-stubseditome-common-javaeditbio-formats-examplesedit.gitmoduleseditome-mdbtoolseditbioformatsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit9b0d2b4d9eb8827f1931b572478ad7b1f39a78391775294593000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-04 09:23:13 +00009b0d2b4d9eb8827f1931b572478ad7b1f39a7839Update component versionseditome-poieditbio-formats-exampleseditbioformatseditome-metakiteditbio-formats-documentationeditome-modeleditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 114114BIOFORMATS-buildjob/BIOFORMATS-build/11486bd4067f579b51aef97560415cca872373cd0e086bd4067f579b51aef97560415cca872373cd0e0origin/merge_ci86bd4067f579b51aef97560415cca872373cd0e086bd4067f579b51aef97560415cca872373cd0e0origin/merge_ci86bd4067f579b51aef97560415cca872373cd0e086bd4067f579b51aef97560415cca872373cd0e0origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#114131586128153BIOFORMATS-build » testintegration #114114falsefalse1144515SUCCESS1775261114790https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/114/testintegrationb6bd8c392ca6e2b0125ecac4b330b3b7e284e4661775260824000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#118 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/118/) 2026-04-04 00:00:24 +0000b6bd8c392ca6e2b0125ecac4b330b3b7e284e466merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitb087fb8f9f7d899640c8c4f80068db8c16194d171775261006000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#118 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/118/) 2026-04-04 00:03:26 +0000b087fb8f9f7d899640c8c4f80068db8c16194d17merge master -Dorg -Ssuccess-onlyedit.gitmoduleseditome-jaieditome-modeleditome-codecseditbioformatseditome-common-javaeditome-metakiteditZarrReadereditbio-formats-exampleseditome-stubseditome-mdbtoolseditbio-formats-documentationeditome-poibioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit86bd4067f579b51aef97560415cca872373cd0e01775261105000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-04 00:05:05 +000086bd4067f579b51aef97560415cca872373cd0e0Update component versionseditbio-formats-documentationeditbioformatseditbio-formats-exampleseditome-metakiteditome-modeleditome-codecseditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 113113BIOFORMATS-buildjob/BIOFORMATS-build/113851a3eaf60be5a14e9c00d50807fef5f18eb6f87851a3eaf60be5a14e9c00d50807fef5f18eb6f87origin/merge_ci851a3eaf60be5a14e9c00d50807fef5f18eb6f87851a3eaf60be5a14e9c00d50807fef5f18eb6f87origin/merge_ci851a3eaf60be5a14e9c00d50807fef5f18eb6f87851a3eaf60be5a14e9c00d50807fef5f18eb6f87origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#113129133128153BIOFORMATS-build » testintegration #113113falsefalse1134474SUCCESS1775203173307https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/113/testintegration4bfef161a145b73f0b3699c9da61a3de33d9f5b21775202871000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#117 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/117/) 2026-04-03 07:54:31 +00004bfef161a145b73f0b3699c9da61a3de33d9f5b2merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit2e125bd015d9a5e252ee75f1d7970eb9921c27b21775203058000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#117 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/117/) 2026-04-03 07:57:38 +00002e125bd015d9a5e252ee75f1d7970eb9921c27b2merge master -Dorg -Ssuccess-onlyeditome-codecseditZarrReadereditbio-formats-exampleseditome-mdbtoolseditome-jaieditbio-formats-documentationeditome-metakitedit.gitmoduleseditome-common-javaeditome-modeleditome-poieditome-stubseditbioformatsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit851a3eaf60be5a14e9c00d50807fef5f18eb6f871775203162000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-03 07:59:22 +0000851a3eaf60be5a14e9c00d50807fef5f18eb6f87Update component versionseditbio-formats-exampleseditome-poieditbioformatseditome-metakiteditome-modeleditbio-formats-documentationeditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 112112BIOFORMATS-buildjob/BIOFORMATS-build/112c0187ea0fa8544bb067f4cf953a8005ae4f7182cc0187ea0fa8544bb067f4cf953a8005ae4f7182corigin/merge_cic0187ea0fa8544bb067f4cf953a8005ae4f7182cc0187ea0fa8544bb067f4cf953a8005ae4f7182corigin/merge_cic0187ea0fa8544bb067f4cf953a8005ae4f7182cc0187ea0fa8544bb067f4cf953a8005ae4f7182corigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#112129431128153BIOFORMATS-build » testintegration #112112falsefalse1124459SUCCESS1775174717601https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/112/testintegration199294b5704023bd44ac34285bcb905d0b33f00b1775174421000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#116 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/116/) 2026-04-03 00:00:21 +0000199294b5704023bd44ac34285bcb905d0b33f00bmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit69c73dab795e2c74aa295850d2778c98c995f3861775174606000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#116 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/116/) 2026-04-03 00:03:26 +000069c73dab795e2c74aa295850d2778c98c995f386merge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditome-codecsedit.gitmoduleseditome-modeleditome-common-javaeditome-mdbtoolseditZarrReadereditome-metakiteditbio-formats-exampleseditome-poieditome-jaieditome-stubseditbioformatsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitc0187ea0fa8544bb067f4cf953a8005ae4f7182c1775174707000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-03 00:05:07 +0000c0187ea0fa8544bb067f4cf953a8005ae4f7182cUpdate component versionseditbio-formats-documentationeditbio-formats-exampleseditome-poieditbioformatseditome-metakiteditome-codecseditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 111111BIOFORMATS-buildjob/BIOFORMATS-build/11152e5ff03449840017403efdce21c74b33b5b800e52e5ff03449840017403efdce21c74b33b5b800eorigin/merge_ci52e5ff03449840017403efdce21c74b33b5b800e52e5ff03449840017403efdce21c74b33b5b800eorigin/merge_ci52e5ff03449840017403efdce21c74b33b5b800e52e5ff03449840017403efdce21c74b33b5b800eorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#111129456128153BIOFORMATS-build » testintegration #111111falsefalse1114444SUCCESS1775132236578https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/111/testintegration1e5a7cf849cb8c15595628fdf40b9936d28b09451775131925000https://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#115 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/115/) 2026-04-02 12:12:05 +00001e5a7cf849cb8c15595628fdf40b9936d28b0945merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitbb50150fe1174995019206d9e1b3fdc0b8ef7cf71775132126000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#115 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/115/) 2026-04-02 12:15:26 +0000bb50150fe1174995019206d9e1b3fdc0b8ef7cf7merge master -Dorg -Ssuccess-onlyeditZarrReadereditome-metakiteditome-stubseditbio-formats-documentationeditome-codecseditbio-formats-exampleseditome-modeleditome-jaieditome-common-javaeditome-poieditbioformatseditome-mdbtoolsedit.gitmodulesbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit52e5ff03449840017403efdce21c74b33b5b800e1775132225000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-02 12:17:05 +000052e5ff03449840017403efdce21c74b33b5b800eUpdate component versionseditome-modeleditome-poieditbio-formats-exampleseditome-codecseditbioformatseditbio-formats-documentationeditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 110110BIOFORMATS-buildjob/BIOFORMATS-build/110525239a5271c6f2890ee7b3cc02553b58001fb64525239a5271c6f2890ee7b3cc02553b58001fb64origin/merge_ci525239a5271c6f2890ee7b3cc02553b58001fb64525239a5271c6f2890ee7b3cc02553b58001fb64origin/merge_ci525239a5271c6f2890ee7b3cc02553b58001fb64525239a5271c6f2890ee7b3cc02553b58001fb64origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#110130487128153BIOFORMATS-build » testintegration #110110falsefalse1104426SUCCESS1775128211471https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/110/testintegrationa8c0de280a0c7505ded8c66ee5dd3ddad7515c4c1775127900000https://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#114 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/114/) 2026-04-02 11:05:00 +0000a8c0de280a0c7505ded8c66ee5dd3ddad7515c4cmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitaba20b36deee5c6176710a9978cc18c5fea8b7241775128102000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#114 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/114/) 2026-04-02 11:08:22 +0000aba20b36deee5c6176710a9978cc18c5fea8b724merge master -Dorg -Ssuccess-onlyeditome-mdbtoolseditome-codecseditome-common-javaeditbio-formats-documentationeditbioformatseditome-jaieditome-poieditome-modeledit.gitmoduleseditbio-formats-exampleseditome-metakiteditZarrReadereditome-stubsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit525239a5271c6f2890ee7b3cc02553b58001fb641775128203000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-02 11:10:03 +0000525239a5271c6f2890ee7b3cc02553b58001fb64Update component versionseditbio-formats-exampleseditome-modeleditome-poieditome-metakiteditome-codecseditbio-formats-documentationeditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 109109BIOFORMATS-buildjob/BIOFORMATS-build/1090a364b8a0266741b2697cd59e4467b5f15da10b50a364b8a0266741b2697cd59e4467b5f15da10b5origin/merge_ci0a364b8a0266741b2697cd59e4467b5f15da10b50a364b8a0266741b2697cd59e4467b5f15da10b5origin/merge_ci0a364b8a0266741b2697cd59e4467b5f15da10b50a364b8a0266741b2697cd59e4467b5f15da10b5origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#109132867128153BIOFORMATS-build » testintegration #109109falsefalse1094408SUCCESS1775122166307https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/109/testintegrationb895b7a1821f6d5d9e25a7a90ea279ac39445c861775121864000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#113 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/113/) 2026-04-02 09:24:24 +0000b895b7a1821f6d5d9e25a7a90ea279ac39445c86merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit3742502d01918d00ec0785cf581c16f125856f491775122059000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#113 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/113/) 2026-04-02 09:27:39 +00003742502d01918d00ec0785cf581c16f125856f49merge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditome-poieditome-stubseditome-codecseditbioformatseditbio-formats-documentationeditome-mdbtoolseditome-metakiteditome-common-javaeditZarrReadereditome-modeledit.gitmoduleseditome-jaibioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit0a364b8a0266741b2697cd59e4467b5f15da10b51775122156000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-02 09:29:16 +00000a364b8a0266741b2697cd59e4467b5f15da10b5Update component versionseditbioformatseditbio-formats-exampleseditome-codecseditome-poieditome-metakiteditome-modeleditbio-formats-documentationgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 108108BIOFORMATS-buildjob/BIOFORMATS-build/108215200a01cb253b4a3af49ce7c1c670124f78a3f215200a01cb253b4a3af49ce7c1c670124f78a3forigin/merge_ci215200a01cb253b4a3af49ce7c1c670124f78a3f215200a01cb253b4a3af49ce7c1c670124f78a3forigin/merge_ci215200a01cb253b4a3af49ce7c1c670124f78a3f215200a01cb253b4a3af49ce7c1c670124f78a3forigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#108139260128153BIOFORMATS-build » testintegration #108108falsefalse1084363SUCCESS1775088320437https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/108/testintegration6a270240e11730b81c11a85687e42bb6b11d7a011775088023000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#112 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/112/) 2026-04-02 00:00:23 +00006a270240e11730b81c11a85687e42bb6b11d7a01merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit85523c1c3d99eaf107ae61126bac6df892b80bef1775088213000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#112 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/112/) 2026-04-02 00:03:33 +000085523c1c3d99eaf107ae61126bac6df892b80befmerge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditome-common-javaedit.gitmoduleseditome-modeleditome-poieditome-jaieditome-metakiteditome-codecseditome-stubseditbio-formats-documentationeditome-mdbtoolseditZarrReadereditbioformatsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit215200a01cb253b4a3af49ce7c1c670124f78a3f1775088311000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-02 00:05:11 +0000215200a01cb253b4a3af49ce7c1c670124f78a3fUpdate component versionseditbio-formats-documentationeditome-metakiteditbio-formats-exampleseditbioformatseditome-poieditome-modeleditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 107107BIOFORMATS-buildjob/BIOFORMATS-build/107ed4bd3282f75f8be0fe7b6ee2f804048135e9d2eed4bd3282f75f8be0fe7b6ee2f804048135e9d2eorigin/merge_cied4bd3282f75f8be0fe7b6ee2f804048135e9d2eed4bd3282f75f8be0fe7b6ee2f804048135e9d2eorigin/merge_cied4bd3282f75f8be0fe7b6ee2f804048135e9d2eed4bd3282f75f8be0fe7b6ee2f804048135e9d2eorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#107238948128153BIOFORMATS-build » testintegration #107107falsefalse1074342SUCCESS1775002018102https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/107/testintegration3dbc9646773746e9f48e386705548f982be520d31775001664000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#111 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/111/) 2026-04-01 00:01:04 +00003dbc9646773746e9f48e386705548f982be520d3merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit22f7836c6e2e6f71f716c894432deba67e6c42971775001862000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#111 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/111/) 2026-04-01 00:04:22 +000022f7836c6e2e6f71f716c894432deba67e6c4297merge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditbioformatseditome-jaieditbio-formats-documentationedit.gitmoduleseditome-modeleditome-stubseditome-common-javaeditZarrReadereditome-codecseditome-poieditome-mdbtoolseditome-metakitbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakited4bd3282f75f8be0fe7b6ee2f804048135e9d2e1775002007000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-01 00:06:47 +0000ed4bd3282f75f8be0fe7b6ee2f804048135e9d2eUpdate component versionseditbio-formats-documentationeditbio-formats-exampleseditome-poieditbioformatseditome-modeleditome-codecseditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 106106BIOFORMATS-buildjob/BIOFORMATS-build/106b1a0778fccfd719121456bb732f3ac11da879addb1a0778fccfd719121456bb732f3ac11da879addorigin/merge_cib1a0778fccfd719121456bb732f3ac11da879addb1a0778fccfd719121456bb732f3ac11da879addorigin/merge_cib1a0778fccfd719121456bb732f3ac11da879addb1a0778fccfd719121456bb732f3ac11da879addorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#106128512128153BIOFORMATS-build » testintegration #106106falsefalse1064276SUCCESS1774915531353https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/106/testintegration0629ffc6c5929ad4b39819a320c7ae30a94dff9a1774915225000https://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#110 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/110/) 2026-03-31 00:00:25 +00000629ffc6c5929ad4b39819a320c7ae30a94dff9amerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit73b38b58f7d3b83234a9895c0601023d073db97d1774915415000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#110 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/110/) 2026-03-31 00:03:35 +000073b38b58f7d3b83234a9895c0601023d073db97dmerge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditome-codecseditome-modeledit.gitmoduleseditome-poieditome-metakiteditZarrReadereditome-jaieditome-mdbtoolseditome-common-javaeditbioformatseditbio-formats-documentationeditome-stubsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitb1a0778fccfd719121456bb732f3ac11da879add1774915523000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-31 00:05:23 +0000b1a0778fccfd719121456bb732f3ac11da879addUpdate component versionseditome-modeleditbio-formats-exampleseditbio-formats-documentationeditbioformatseditome-poieditome-codecseditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 105105BIOFORMATS-buildjob/BIOFORMATS-build/1052095c7aabcab9bb88fc5912f35049e4168e0eddc2095c7aabcab9bb88fc5912f35049e4168e0eddcorigin/merge_ci2095c7aabcab9bb88fc5912f35049e4168e0eddc2095c7aabcab9bb88fc5912f35049e4168e0eddcorigin/merge_ci2095c7aabcab9bb88fc5912f35049e4168e0eddc2095c7aabcab9bb88fc5912f35049e4168e0eddcorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#105130454128153BIOFORMATS-build » testintegration #105105falsefalse1054240SUCCESS1774829159302https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/105/testintegration4dbc50732d3156618b6632c3c5d536b3365e5a9a1774828825000https://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#109 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/109/) 2026-03-30 00:00:25 +00004dbc50732d3156618b6632c3c5d536b3365e5a9amerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit0eabd934f489d7b6346c980f4343e3d4de9c345e1774829025000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#109 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/109/) 2026-03-30 00:03:45 +00000eabd934f489d7b6346c980f4343e3d4de9c345emerge master -Dorg -Ssuccess-onlyeditome-metakiteditome-modeleditome-stubseditome-common-javaeditbio-formats-exampleseditZarrReadereditbio-formats-documentationeditome-jaieditome-mdbtoolseditome-codecseditome-poiedit.gitmoduleseditbioformatsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit2095c7aabcab9bb88fc5912f35049e4168e0eddc1774829147000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-30 00:05:47 +00002095c7aabcab9bb88fc5912f35049e4168e0eddcUpdate component versionseditome-metakiteditome-poieditome-codecseditbio-formats-exampleseditbio-formats-documentationeditome-modeleditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 104104BIOFORMATS-buildjob/BIOFORMATS-build/1047f9f174924c6022992177d474efa267188cfa5ee7f9f174924c6022992177d474efa267188cfa5eeorigin/merge_ci7f9f174924c6022992177d474efa267188cfa5ee7f9f174924c6022992177d474efa267188cfa5eeorigin/merge_ci7f9f174924c6022992177d474efa267188cfa5ee7f9f174924c6022992177d474efa267188cfa5eeorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#104131057128153BIOFORMATS-build » testintegration #104104falsefalse1044204SUCCESS1774742712139https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/104/testintegration07678f66e53dfae304f4ef2a90d43e0e69ebe98f1774742421000https://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#108 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/108/) 2026-03-29 00:00:21 +000007678f66e53dfae304f4ef2a90d43e0e69ebe98fmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit0a6a006bae36b72adc6d30e48b10c14207217ffd1774742603000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#108 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/108/) 2026-03-29 00:03:23 +00000a6a006bae36b72adc6d30e48b10c14207217ffdmerge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditome-codecseditome-metakiteditome-poieditome-stubsedit.gitmoduleseditome-modeleditZarrReadereditome-jaieditbioformatseditome-mdbtoolseditbio-formats-documentationeditome-common-javabioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit7f9f174924c6022992177d474efa267188cfa5ee1774742701000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-29 00:05:01 +00007f9f174924c6022992177d474efa267188cfa5eeUpdate component versionseditbioformatseditome-poieditome-metakiteditbio-formats-exampleseditome-codecseditome-modeleditbio-formats-documentationgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 103103BIOFORMATS-buildjob/BIOFORMATS-build/103c96686b71900922f0baa8b1d72a4940c919749a7c96686b71900922f0baa8b1d72a4940c919749a7origin/merge_cic96686b71900922f0baa8b1d72a4940c919749a7c96686b71900922f0baa8b1d72a4940c919749a7origin/merge_cic96686b71900922f0baa8b1d72a4940c919749a7c96686b71900922f0baa8b1d72a4940c919749a7origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#103131478128153BIOFORMATS-build » testintegration #103103falsefalse1034168SUCCESS1774656324983https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/103/testintegrationea53845bef7195a7f7b78ceed1039382ae1f2b0f1774656023000https://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#107 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/107/) 2026-03-28 00:00:23 +0000ea53845bef7195a7f7b78ceed1039382ae1f2b0fmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitef5ae4cb0087308a34beb8871d6f83adc8509b671774656209000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#107 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/107/) 2026-03-28 00:03:29 +0000ef5ae4cb0087308a34beb8871d6f83adc8509b67merge master -Dorg -Ssuccess-onlyeditome-metakiteditbio-formats-documentationeditome-modeleditome-mdbtoolseditome-poieditZarrReadereditome-jaieditbioformatseditome-codecseditbio-formats-examplesedit.gitmoduleseditome-common-javaeditome-stubsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitc96686b71900922f0baa8b1d72a4940c919749a71774656313000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-28 00:05:13 +0000c96686b71900922f0baa8b1d72a4940c919749a7Update component versionseditbio-formats-exampleseditome-codecseditbioformatseditome-poieditbio-formats-documentationeditome-modeleditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 102102BIOFORMATS-buildjob/BIOFORMATS-build/102c8c33e82153ed2d8dac4984f12ddd42bf43990e2c8c33e82153ed2d8dac4984f12ddd42bf43990e2origin/merge_cic8c33e82153ed2d8dac4984f12ddd42bf43990e2c8c33e82153ed2d8dac4984f12ddd42bf43990e2origin/merge_cic8c33e82153ed2d8dac4984f12ddd42bf43990e2c8c33e82153ed2d8dac4984f12ddd42bf43990e2origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#102133560128153BIOFORMATS-build » testintegration #102102falsefalse1024130SUCCESS1774569922857https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/102/testintegrationaaa943403b0485723d49c1c969b119435cf70afe1774569621000https://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#106 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/106/) 2026-03-27 00:00:21 +0000aaa943403b0485723d49c1c969b119435cf70afemerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit4f63dacb77830106b5833ac5ce99e9f9ab7a03e51774569808000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#106 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/106/) 2026-03-27 00:03:28 +00004f63dacb77830106b5833ac5ce99e9f9ab7a03e5merge master -Dorg -Ssuccess-onlyeditome-common-javaeditZarrReaderedit.gitmoduleseditome-metakiteditbio-formats-documentationeditome-mdbtoolseditome-jaieditome-poieditome-stubseditbioformatseditome-codecseditome-modeleditbio-formats-examplesbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitc8c33e82153ed2d8dac4984f12ddd42bf43990e21774569910000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-27 00:05:10 +0000c8c33e82153ed2d8dac4984f12ddd42bf43990e2Update component versionseditome-poieditbio-formats-exampleseditome-metakiteditome-modeleditbioformatseditbio-formats-documentationeditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 101101BIOFORMATS-buildjob/BIOFORMATS-build/1012a5b593537bdc4f93f7f94d7104d4e7918bdae1b2a5b593537bdc4f93f7f94d7104d4e7918bdae1borigin/merge_ci2a5b593537bdc4f93f7f94d7104d4e7918bdae1b2a5b593537bdc4f93f7f94d7104d4e7918bdae1borigin/merge_ci2a5b593537bdc4f93f7f94d7104d4e7918bdae1b2a5b593537bdc4f93f7f94d7104d4e7918bdae1borigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#101135382128153BIOFORMATS-build » testintegration #101101falsefalse1014087SUCCESS1774483520690https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/101/testintegration1df279de37638c373ec94cafb883b84c53273f2d1774483224000https://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#105 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/105/) 2026-03-26 00:00:24 +00001df279de37638c373ec94cafb883b84c53273f2dmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitd5647cb3c6f58a7c446d5bccaeb0df9cd0308ca21774483410000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#105 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/105/) 2026-03-26 00:03:30 +0000d5647cb3c6f58a7c446d5bccaeb0df9cd0308ca2merge master -Dorg -Ssuccess-onlyeditome-jaieditbioformatseditZarrReadereditome-metakiteditome-poieditbio-formats-documentationeditome-codecseditbio-formats-examplesedit.gitmoduleseditome-mdbtoolseditome-stubseditome-modeleditome-common-javabioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit2a5b593537bdc4f93f7f94d7104d4e7918bdae1b1774483510000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-26 00:05:10 +00002a5b593537bdc4f93f7f94d7104d4e7918bdae1bUpdate component versionseditbioformatseditome-poieditbio-formats-exampleseditome-modeleditbio-formats-documentationeditome-codecseditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 100100BIOFORMATS-buildjob/BIOFORMATS-build/100890de877697b0ac30f727d1a65d9ffde34014653890de877697b0ac30f727d1a65d9ffde34014653origin/merge_ci890de877697b0ac30f727d1a65d9ffde34014653890de877697b0ac30f727d1a65d9ffde34014653origin/merge_ci890de877697b0ac30f727d1a65d9ffde34014653890de877697b0ac30f727d1a65d9ffde34014653origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#100224177128153BIOFORMATS-build » testintegration #100100falsefalse1004043SUCCESS1774397173334https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/100/testintegration3c592c435fd3eebaa31fb21de55aabbe7a4264b31774396858000https://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#104 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/104/) 2026-03-25 00:00:58 +00003c592c435fd3eebaa31fb21de55aabbe7a4264b3merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit6561ce61ada8b58cf5b50db54cb904abd489e28b1774397054000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..33507782 Previously merged: - 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 465 pwalczysko 'Ignore umassmed.edu, 403' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#104 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/104/) 2026-03-25 00:04:14 +00006561ce61ada8b58cf5b50db54cb904abd489e28bmerge master -Dorg -Ssuccess-onlyeditome-poieditome-common-javaeditome-codecseditome-jaieditome-stubseditbio-formats-documentationeditome-mdbtoolseditome-modeledit.gitmoduleseditZarrReadereditbioformatseditbio-formats-exampleseditome-metakitbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit890de877697b0ac30f727d1a65d9ffde340146531774397162000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-25 00:06:02 +0000890de877697b0ac30f727d1a65d9ffde34014653Update component versionseditbio-formats-exampleseditbioformatseditome-codecseditome-metakiteditome-modeleditome-poieditbio-formats-documentationgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 9999BIOFORMATS-buildjob/BIOFORMATS-build/9901371a03d2c93c219e3dd6a42ae92946c680d20f01371a03d2c93c219e3dd6a42ae92946c680d20forigin/merge_ci01371a03d2c93c219e3dd6a42ae92946c680d20f01371a03d2c93c219e3dd6a42ae92946c680d20forigin/merge_ci01371a03d2c93c219e3dd6a42ae92946c680d20f01371a03d2c93c219e3dd6a42ae92946c680d20forigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#99126181128153BIOFORMATS-build » testintegration #9999falsefalse993999SUCCESS1774310722523https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/99/testintegrationdc24e57a2e7904edfbece963b65c567d50f355b01774310421000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#103 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/103/) 2026-03-24 00:00:21 +0000dc24e57a2e7904edfbece963b65c567d50f355b0merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit341ece09541e3a528abe0246399baa897abcdb771774310614000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..33507782 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#103 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/103/) 2026-03-24 00:03:34 +0000341ece09541e3a528abe0246399baa897abcdb77merge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditZarrReadereditome-mdbtoolseditome-poiedit.gitmoduleseditome-common-javaeditbio-formats-exampleseditome-stubseditbioformatseditome-jaieditome-modeleditome-codecseditome-metakitbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit01371a03d2c93c219e3dd6a42ae92946c680d20f1774310715000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-24 00:05:15 +000001371a03d2c93c219e3dd6a42ae92946c680d20fUpdate component versionseditbio-formats-exampleseditome-poieditome-modeleditome-metakiteditome-codecseditbio-formats-documentationeditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 9898BIOFORMATS-buildjob/BIOFORMATS-build/98249fa5d7d5d0dc07c9e575443388cee57b486980249fa5d7d5d0dc07c9e575443388cee57b486980origin/merge_ci249fa5d7d5d0dc07c9e575443388cee57b486980249fa5d7d5d0dc07c9e575443388cee57b486980origin/merge_ci249fa5d7d5d0dc07c9e575443388cee57b486980249fa5d7d5d0dc07c9e575443388cee57b486980origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#98129341128153BIOFORMATS-build » testintegration #9898falsefalse983955SUCCESS1774224320396https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/98/testintegrationf87f0c477182c39aed976b9eecb5d3d8537e419f1774224023000https://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#102 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/102/) 2026-03-23 00:00:23 +0000f87f0c477182c39aed976b9eecb5d3d8537e419fmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit7bfb26ce2c13c62659283c2eaf3821b5f17787961774224203000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..e8001c59 Previously merged: - 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 463 pwalczysko 'Ignore zenodo 403' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#102 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/102/) 2026-03-23 00:03:23 +00007bfb26ce2c13c62659283c2eaf3821b5f1778796merge master -Dorg -Ssuccess-onlyeditbio-formats-exampleseditome-modeleditome-metakiteditome-jaieditbioformatseditome-codecsedit.gitmoduleseditome-common-javaeditbio-formats-documentationeditZarrReadereditome-poieditome-mdbtoolseditome-stubsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit249fa5d7d5d0dc07c9e575443388cee57b4869801774224309000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-23 00:05:09 +0000249fa5d7d5d0dc07c9e575443388cee57b486980Update component versionseditbio-formats-documentationeditome-metakiteditome-poieditome-codecseditbioformatseditome-modeleditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 9797BIOFORMATS-buildjob/BIOFORMATS-build/97acc73a90d25612e47ce7e431afb450fc03c0dc70acc73a90d25612e47ce7e431afb450fc03c0dc70origin/merge_ciacc73a90d25612e47ce7e431afb450fc03c0dc70acc73a90d25612e47ce7e431afb450fc03c0dc70origin/merge_ciacc73a90d25612e47ce7e431afb450fc03c0dc70acc73a90d25612e47ce7e431afb450fc03c0dc70origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#97132523128153BIOFORMATS-build » testintegration #9797falsefalse973911SUCCESS1774137908328https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/97/testintegration403d852239b40f42fbe4f625ad10655e81b334f01774137622000https://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#101 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/101/) 2026-03-22 00:00:22 +0000403d852239b40f42fbe4f625ad10655e81b334f0merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit57b9faaad76a5f65ada70d1fb07f69efae7ce4271774137803000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..e8001c59 Previously merged: - 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 463 pwalczysko 'Ignore zenodo 403' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#101 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/101/) 2026-03-22 00:03:23 +000057b9faaad76a5f65ada70d1fb07f69efae7ce427merge master -Dorg -Ssuccess-onlyeditome-jaieditbio-formats-exampleseditome-common-javaeditbioformatseditome-modeledit.gitmoduleseditZarrReadereditome-codecseditome-metakiteditbio-formats-documentationeditome-mdbtoolseditome-poieditome-stubsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitacc73a90d25612e47ce7e431afb450fc03c0dc701774137900000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-22 00:05:00 +0000acc73a90d25612e47ce7e431afb450fc03c0dc70Update component versionseditome-modeleditbio-formats-documentationeditome-poieditbio-formats-exampleseditome-metakiteditbioformatseditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 9696BIOFORMATS-buildjob/BIOFORMATS-build/96f4f2f34b6b2c438697e7cb7e33fa60b2bc080ac5f4f2f34b6b2c438697e7cb7e33fa60b2bc080ac5origin/merge_cif4f2f34b6b2c438697e7cb7e33fa60b2bc080ac5f4f2f34b6b2c438697e7cb7e33fa60b2bc080ac5origin/merge_cif4f2f34b6b2c438697e7cb7e33fa60b2bc080ac5f4f2f34b6b2c438697e7cb7e33fa60b2bc080ac5origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#96129909128153BIOFORMATS-build » testintegration #9696falsefalse963867SUCCESS1774051511258https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/96/testintegrationc252ea2cd61969d65c3b080992ca506773ad155a1774051220000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#100 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/100/) 2026-03-21 00:00:20 +0000c252ea2cd61969d65c3b080992ca506773ad155amerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitf4b403862bb5315673afce199e8d5c06d58622981774051402000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..e8001c59 Previously merged: - 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 463 pwalczysko 'Ignore zenodo 403' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#100 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/100/) 2026-03-21 00:03:22 +0000f4b403862bb5315673afce199e8d5c06d5862298merge master -Dorg -Ssuccess-onlyeditbioformatseditbio-formats-documentationeditome-metakiteditome-modeleditbio-formats-exampleseditome-codecseditome-stubseditome-jaieditome-poieditome-mdbtoolseditZarrReadereditome-common-javaedit.gitmodulesbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitf4f2f34b6b2c438697e7cb7e33fa60b2bc080ac51774051500000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-21 00:05:00 +0000f4f2f34b6b2c438697e7cb7e33fa60b2bc080ac5Update component versionseditbio-formats-exampleseditome-codecseditbio-formats-documentationeditbioformatseditome-modeleditome-poieditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 9595BIOFORMATS-buildjob/BIOFORMATS-build/9563cf4541ccd9e19b4623b429d95e9512a1ecf12463cf4541ccd9e19b4623b429d95e9512a1ecf124origin/merge_ci63cf4541ccd9e19b4623b429d95e9512a1ecf12463cf4541ccd9e19b4623b429d95e9512a1ecf124origin/merge_ci63cf4541ccd9e19b4623b429d95e9512a1ecf12463cf4541ccd9e19b4623b429d95e9512a1ecf124origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#95136230128153BIOFORMATS-build » testintegration #9595falsefalse953823SUCCESS1773965124118https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/95/testintegrationbc19e5cda101add243ecebc5bd1abfc5b2ec79611773964822000https://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#99 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/99/) 2026-03-20 00:00:22 +0000bc19e5cda101add243ecebc5bd1abfc5b2ec7961merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakiteaaa415c0cdae85e4751fc9a20244a31dbdc409e1773965005000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..e8001c59 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#99 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/99/) 2026-03-20 00:03:25 +0000eaaa415c0cdae85e4751fc9a20244a31dbdc409emerge master -Dorg -Ssuccess-onlyeditome-poieditome-mdbtoolseditbioformatseditome-common-javaeditome-jaieditome-codecseditome-stubsedit.gitmoduleseditome-modeleditome-metakiteditZarrReadereditbio-formats-documentationeditbio-formats-examplesbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit63cf4541ccd9e19b4623b429d95e9512a1ecf1241773965114000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-20 00:05:14 +000063cf4541ccd9e19b4623b429d95e9512a1ecf124Update component versionseditome-codecseditbio-formats-exampleseditbioformatseditome-modeleditome-poieditbio-formats-documentationeditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 9494BIOFORMATS-buildjob/BIOFORMATS-build/94ece6ac423d658d25b2412e9612ca75dc6fae0fc0ece6ac423d658d25b2412e9612ca75dc6fae0fc0origin/merge_ciece6ac423d658d25b2412e9612ca75dc6fae0fc0ece6ac423d658d25b2412e9612ca75dc6fae0fc0origin/merge_ciece6ac423d658d25b2412e9612ca75dc6fae0fc0ece6ac423d658d25b2412e9612ca75dc6fae0fc0origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#94139044128153BIOFORMATS-build » testintegration #9494falsefalse943779SUCCESS1773878717028https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/94/testintegration9ba62b2eb40185bf4967d3b47966f50aec1136931773878421000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#98 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/98/) 2026-03-19 00:00:21 +00009ba62b2eb40185bf4967d3b47966f50aec113693merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit8d5f324b6aa45756eb1349f2cf6fd9624fb655061773878606000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..e8001c59 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#98 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/98/) 2026-03-19 00:03:26 +00008d5f324b6aa45756eb1349f2cf6fd9624fb65506merge master -Dorg -Ssuccess-onlyeditZarrReadereditome-codecseditome-stubseditbioformatseditbio-formats-documentationeditome-jaieditbio-formats-exampleseditome-metakiteditome-poiedit.gitmoduleseditome-mdbtoolseditome-modeleditome-common-javabioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitece6ac423d658d25b2412e9612ca75dc6fae0fc01773878705000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-19 00:05:05 +0000ece6ac423d658d25b2412e9612ca75dc6fae0fc0Update component versionseditome-metakiteditbio-formats-exampleseditome-codecseditbioformatseditome-poieditbio-formats-documentationeditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 9393BIOFORMATS-buildjob/BIOFORMATS-build/93a3ba97f725318bfa206742f20be703cc5cfc5256a3ba97f725318bfa206742f20be703cc5cfc5256origin/merge_cia3ba97f725318bfa206742f20be703cc5cfc5256a3ba97f725318bfa206742f20be703cc5cfc5256origin/merge_cia3ba97f725318bfa206742f20be703cc5cfc5256a3ba97f725318bfa206742f20be703cc5cfc5256origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#93223724128153BIOFORMATS-build » testintegration #9393falsefalse933733SUCCESS1773792369840https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/93/testintegrationc0f8433b1d8022600892c882635887f2b2be68161773792054000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#97 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/97/) 2026-03-18 00:00:54 +0000c0f8433b1d8022600892c882635887f2b2be6816merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit80f0a868e856e5ff363274694199004381a7443f1773792248000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..7ab05cc9 Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 461 melissalinkert 'Release notes for 8.5.0' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..d51c6f859f Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#97 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/97/) 2026-03-18 00:04:08 +000080f0a868e856e5ff363274694199004381a7443fmerge master -Dorg -Ssuccess-onlyeditbioformatseditome-stubseditome-metakitedit.gitmoduleseditome-codecseditbio-formats-documentationeditome-poieditbio-formats-exampleseditZarrReadereditome-common-javaeditome-mdbtoolseditome-modeleditome-jaibioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakita3ba97f725318bfa206742f20be703cc5cfc52561773792356000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-18 00:05:56 +0000a3ba97f725318bfa206742f20be703cc5cfc5256Update component versionseditome-codecseditome-metakiteditbio-formats-exampleseditome-poieditbioformatseditbio-formats-documentationeditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 9292BIOFORMATS-buildjob/BIOFORMATS-build/92d670ccf10c2c084c221d7f08de5dc0d90556f5c9d670ccf10c2c084c221d7f08de5dc0d90556f5c9origin/merge_cid670ccf10c2c084c221d7f08de5dc0d90556f5c9d670ccf10c2c084c221d7f08de5dc0d90556f5c9origin/merge_cid670ccf10c2c084c221d7f08de5dc0d90556f5c9d670ccf10c2c084c221d7f08de5dc0d90556f5c9origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#92128302128153BIOFORMATS-build » testintegration #9292falsefalse923689SUCCESS1773705922055https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/92/testintegration9d08b7cadf2e0b8bf86d1e8a0a4712f4bc0b0b6a1773705621000https://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#96 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/96/) 2026-03-17 00:00:21 +00009d08b7cadf2e0b8bf86d1e8a0a4712f4bc0b0b6amerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitfa57fbf8b1efbf525658b0434701a3cdbc671c731773705809000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..602343a3 Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 461 melissalinkert 'Release notes for 8.5.0' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4f37585ebc Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#96 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/96/) 2026-03-17 00:03:29 +0000fa57fbf8b1efbf525658b0434701a3cdbc671c73merge master -Dorg -Ssuccess-onlyeditome-codecseditome-common-javaedit.gitmoduleseditbioformatseditbio-formats-exampleseditome-jaieditbio-formats-documentationeditome-modeleditZarrReadereditome-metakiteditome-poieditome-stubseditome-mdbtoolsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitd670ccf10c2c084c221d7f08de5dc0d90556f5c91773705911000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-17 00:05:11 +0000d670ccf10c2c084c221d7f08de5dc0d90556f5c9Update component versionseditbio-formats-documentationeditome-metakiteditbio-formats-exampleseditbioformatseditome-modeleditome-codecseditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 9191BIOFORMATS-buildjob/BIOFORMATS-build/91f7fd023f90ee5d6c430043fdb43107e81557c86df7fd023f90ee5d6c430043fdb43107e81557c86dorigin/merge_cif7fd023f90ee5d6c430043fdb43107e81557c86df7fd023f90ee5d6c430043fdb43107e81557c86dorigin/merge_cif7fd023f90ee5d6c430043fdb43107e81557c86df7fd023f90ee5d6c430043fdb43107e81557c86dorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#91128099128153BIOFORMATS-build » testintegration #9191falsefalse913674SUCCESS1773619514987https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/91/testintegratione97e69825b07abbac3baa753d39e16289e14fdb61773619224000https://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#95 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/95/) 2026-03-16 00:00:24 +0000e97e69825b07abbac3baa753d39e16289e14fdb6merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit20b0a280180b956464d4bfff93d58ff54e444b4a1773619404000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..602343a3 Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4f37585ebc Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#95 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/95/) 2026-03-16 00:03:24 +000020b0a280180b956464d4bfff93d58ff54e444b4amerge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditbio-formats-exampleseditome-metakiteditZarrReadereditome-common-javaeditome-modeledit.gitmoduleseditbioformatseditome-codecseditome-jaieditome-stubseditome-mdbtoolseditome-poibioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitf7fd023f90ee5d6c430043fdb43107e81557c86d1773619503000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-16 00:05:03 +0000f7fd023f90ee5d6c430043fdb43107e81557c86dUpdate component versionseditome-codecseditome-metakiteditbio-formats-exampleseditome-poieditbioformatseditome-modeleditbio-formats-documentationgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 9090BIOFORMATS-buildjob/BIOFORMATS-build/90a3476c2c30bfcb3f1b4a60211457c838907865c4a3476c2c30bfcb3f1b4a60211457c838907865c4origin/merge_cia3476c2c30bfcb3f1b4a60211457c838907865c4a3476c2c30bfcb3f1b4a60211457c838907865c4origin/merge_cia3476c2c30bfcb3f1b4a60211457c838907865c4a3476c2c30bfcb3f1b4a60211457c838907865c4origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#90129751128153BIOFORMATS-build » testintegration #9090falsefalse903630SUCCESS1773533107831https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/90/testintegration61e8d012b9a4402d4592aa4bfea2c60827b864371773532821000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#94 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/94/) 2026-03-15 00:00:21 +000061e8d012b9a4402d4592aa4bfea2c60827b86437merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit02242915603e081445b9968fba5e00a743f15ba21773533002000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..602343a3 Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4f37585ebc Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#94 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/94/) 2026-03-15 00:03:22 +000002242915603e081445b9968fba5e00a743f15ba2merge master -Dorg -Ssuccess-onlyeditome-codecsedit.gitmoduleseditbio-formats-exampleseditome-jaieditome-common-javaeditome-modeleditbioformatseditome-metakiteditome-mdbtoolseditZarrReadereditome-stubseditome-poieditbio-formats-documentationbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakita3476c2c30bfcb3f1b4a60211457c838907865c41773533100000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-15 00:05:00 +0000a3476c2c30bfcb3f1b4a60211457c838907865c4Update component versionseditome-poieditbio-formats-exampleseditbioformatseditome-codecseditome-metakiteditbio-formats-documentationeditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 8989BIOFORMATS-buildjob/BIOFORMATS-build/8963aab8a1c081d9aa1cacf8540bdb4b6f8706d6d563aab8a1c081d9aa1cacf8540bdb4b6f8706d6d5origin/merge_ci63aab8a1c081d9aa1cacf8540bdb4b6f8706d6d563aab8a1c081d9aa1cacf8540bdb4b6f8706d6d5origin/merge_ci63aab8a1c081d9aa1cacf8540bdb4b6f8706d6d563aab8a1c081d9aa1cacf8540bdb4b6f8706d6d5origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#89129263128153BIOFORMATS-build » testintegration #8989falsefalse893586SUCCESS1773446735647https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/89/testintegration79194ec9f3b6e439c6c6d661e716d221a57fc3071773446424000https://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#93 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/93/) 2026-03-14 00:00:24 +000079194ec9f3b6e439c6c6d661e716d221a57fc307merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit943ca7c2146457b499a0f2a4da5e3cee09d9999d1773446627000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..602343a3 Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4f37585ebc Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#93 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/93/) 2026-03-14 00:03:47 +0000943ca7c2146457b499a0f2a4da5e3cee09d9999dmerge master -Dorg -Ssuccess-onlyeditome-mdbtoolsedit.gitmoduleseditome-common-javaeditome-modeleditbioformatseditbio-formats-exampleseditbio-formats-documentationeditome-jaieditZarrReadereditome-metakiteditome-stubseditome-codecseditome-poibioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit63aab8a1c081d9aa1cacf8540bdb4b6f8706d6d51773446726000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-14 00:05:26 +000063aab8a1c081d9aa1cacf8540bdb4b6f8706d6d5Update component versionseditome-poieditome-metakiteditome-modeleditbio-formats-exampleseditome-codecseditbio-formats-documentationeditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 8888BIOFORMATS-buildjob/BIOFORMATS-build/88b033b820df2717d902ca9cb7219930de1709d06eb033b820df2717d902ca9cb7219930de1709d06eorigin/merge_cib033b820df2717d902ca9cb7219930de1709d06eb033b820df2717d902ca9cb7219930de1709d06eorigin/merge_cib033b820df2717d902ca9cb7219930de1709d06eb033b820df2717d902ca9cb7219930de1709d06eorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#88134252128153BIOFORMATS-build » testintegration #8888falsefalse883542SUCCESS1773360323378https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/88/testintegration2433ca84a79902d328a38659800dbd422b24433a1773360022000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#92 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/92/) 2026-03-13 00:00:22 +00002433ca84a79902d328a38659800dbd422b24433amerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit88cca60e098746e2da7be9bae00d32e85f26c0731773360213000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..602343a3 Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..9054223342 Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - 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' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#92 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/92/) 2026-03-13 00:03:33 +000088cca60e098746e2da7be9bae00d32e85f26c073merge master -Dorg -Ssuccess-onlyeditbioformatseditbio-formats-exampleseditome-mdbtoolseditome-stubseditome-codecseditome-common-javaeditome-modeledit.gitmoduleseditome-jaieditome-metakiteditome-poieditbio-formats-documentationeditZarrReaderbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitb033b820df2717d902ca9cb7219930de1709d06e1773360311000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-13 00:05:11 +0000b033b820df2717d902ca9cb7219930de1709d06eUpdate component versionseditome-poieditome-metakiteditbio-formats-exampleseditbioformatseditbio-formats-documentationeditome-modeleditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 8787BIOFORMATS-buildjob/BIOFORMATS-build/87ba604ae265b277f7560e86babc31506f7acc7411ba604ae265b277f7560e86babc31506f7acc7411origin/merge_ciba604ae265b277f7560e86babc31506f7acc7411ba604ae265b277f7560e86babc31506f7acc7411origin/merge_ciba604ae265b277f7560e86babc31506f7acc7411ba604ae265b277f7560e86babc31506f7acc7411origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#87140404128153BIOFORMATS-build » testintegration #8787falsefalse873497SUCCESS1773273921381https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/87/testintegration2030093e8ac97383cc496238aac3b9130100aa641773273624000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#91 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/91/) 2026-03-12 00:00:24 +00002030093e8ac97383cc496238aac3b9130100aa64merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit7436d88957807c68d32d83af76e441f1984c63351773273812000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..602343a3 Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..9054223342 Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - 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' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#91 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/91/) 2026-03-12 00:03:32 +00007436d88957807c68d32d83af76e441f1984c6335merge master -Dorg -Ssuccess-onlyeditome-codecseditome-mdbtoolseditome-metakiteditbio-formats-exampleseditome-jaieditome-modeleditome-common-javaeditbio-formats-documentationeditbioformatseditome-poieditome-stubsedit.gitmoduleseditZarrReaderbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitba604ae265b277f7560e86babc31506f7acc74111773273911000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-12 00:05:11 +0000ba604ae265b277f7560e86babc31506f7acc7411Update component versionseditome-modeleditbio-formats-documentationeditome-metakiteditbio-formats-exampleseditome-codecseditome-poieditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 8686BIOFORMATS-buildjob/BIOFORMATS-build/86b57211e8e0bf4afbd6eebe4e2af864d0e2456378b57211e8e0bf4afbd6eebe4e2af864d0e2456378origin/merge_cib57211e8e0bf4afbd6eebe4e2af864d0e2456378b57211e8e0bf4afbd6eebe4e2af864d0e2456378origin/merge_cib57211e8e0bf4afbd6eebe4e2af864d0e2456378b57211e8e0bf4afbd6eebe4e2af864d0e2456378origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#86221553128153BIOFORMATS-build » testintegration #8686falsefalse863453SUCCESS1773187574135https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/86/testintegrationf0066e6902b8b31b7bf474131a58513b45574bdd1773187263000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#90 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/90/) 2026-03-11 00:01:03 +0000f0066e6902b8b31b7bf474131a58513b45574bddmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitf204980e0af9837a5e5c1a2570a491e6f05aa9841773187455000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..602343a3 Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..9054223342 Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - 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' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#90 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/90/) 2026-03-11 00:04:15 +0000f204980e0af9837a5e5c1a2570a491e6f05aa984merge master -Dorg -Ssuccess-onlyeditome-modeleditbio-formats-exampleseditbioformatsedit.gitmoduleseditome-common-javaeditome-jaieditZarrReadereditome-mdbtoolseditome-poieditome-metakiteditome-codecseditome-stubseditbio-formats-documentationbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitb57211e8e0bf4afbd6eebe4e2af864d0e24563781773187563000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-11 00:06:03 +0000b57211e8e0bf4afbd6eebe4e2af864d0e2456378Update component versionseditbio-formats-documentationeditome-modeleditome-poieditbioformatseditbio-formats-exampleseditome-codecseditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 8585BIOFORMATS-buildjob/BIOFORMATS-build/8595c3521ea173171ef4db070f59021174b210a49b95c3521ea173171ef4db070f59021174b210a49borigin/merge_ci95c3521ea173171ef4db070f59021174b210a49b95c3521ea173171ef4db070f59021174b210a49borigin/merge_ci95c3521ea173171ef4db070f59021174b210a49b95c3521ea173171ef4db070f59021174b210a49borigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#85130705128153BIOFORMATS-build » testintegration #8585falsefalse853409SUCCESS1773101121295https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/85/testintegration1dbc0200230d9df14dd84c01b033b9db1f4923651773100820000https://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#89 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/89/) 2026-03-10 00:00:20 +00001dbc0200230d9df14dd84c01b033b9db1f492365merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitb018d6692601eaed4e2fa828e7cdb213ff6957ca1773101014000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..1473abf2 Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..9054223342 Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - 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' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#89 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/89/) 2026-03-10 00:03:34 +0000b018d6692601eaed4e2fa828e7cdb213ff6957camerge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditZarrReadereditome-common-javaeditbio-formats-exampleseditbioformatseditome-modeleditome-jaieditome-metakiteditome-poieditome-stubsedit.gitmoduleseditome-mdbtoolseditome-codecsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit95c3521ea173171ef4db070f59021174b210a49b1773101111000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-10 00:05:11 +000095c3521ea173171ef4db070f59021174b210a49bUpdate component versionseditbio-formats-exampleseditbioformatseditome-poieditbio-formats-documentationeditome-codecseditome-modeleditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 8484BIOFORMATS-buildjob/BIOFORMATS-build/84fcca464b580feb5781b802292b276175037a48c9fcca464b580feb5781b802292b276175037a48c9origin/merge_cifcca464b580feb5781b802292b276175037a48c9fcca464b580feb5781b802292b276175037a48c9origin/merge_cifcca464b580feb5781b802292b276175037a48c9fcca464b580feb5781b802292b276175037a48c9origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#84129807128153BIOFORMATS-build » testintegration #8484falsefalse843365SUCCESS1773014709265https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/84/testintegration934b421a6b9dcf31ef0d77967ed5e0b2f2ce63981773014422000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#88 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/88/) 2026-03-09 00:00:22 +0000934b421a6b9dcf31ef0d77967ed5e0b2f2ce6398merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakita421ed94b89a632168ec69803e0887c949e328fa1773014603000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..1473abf2 Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..ec98173a19 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - 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' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#88 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/88/) 2026-03-09 00:03:23 +0000a421ed94b89a632168ec69803e0887c949e328famerge master -Dorg -Ssuccess-onlyeditome-common-javaeditome-poieditome-metakiteditbio-formats-documentationeditbioformatseditome-codecseditome-jaieditbio-formats-exampleseditome-stubsedit.gitmoduleseditZarrReadereditome-mdbtoolseditome-modelbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitfcca464b580feb5781b802292b276175037a48c91773014700000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-09 00:05:00 +0000fcca464b580feb5781b802292b276175037a48c9Update component versionseditome-modeleditome-poieditbio-formats-exampleseditbioformatseditome-metakiteditbio-formats-documentationeditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 8383BIOFORMATS-buildjob/BIOFORMATS-build/8334a02bf417e52b422fb90ac8642aef233ec0f3c934a02bf417e52b422fb90ac8642aef233ec0f3c9origin/merge_ci34a02bf417e52b422fb90ac8642aef233ec0f3c934a02bf417e52b422fb90ac8642aef233ec0f3c9origin/merge_ci34a02bf417e52b422fb90ac8642aef233ec0f3c934a02bf417e52b422fb90ac8642aef233ec0f3c9origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#83133065128153BIOFORMATS-build » testintegration #8383falsefalse833321SUCCESS1772928307163https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/83/testintegrationdd26bd4fc8adf45e4a1aebf936a9be922556c2be1772928021000https://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#87 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/87/) 2026-03-08 00:00:21 +0000dd26bd4fc8adf45e4a1aebf936a9be922556c2bemerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit621b77a21d725254e928ceba9eab3dc3e14e3ebc1772928202000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..1473abf2 Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..ec98173a19 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - 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' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#87 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/87/) 2026-03-08 00:03:22 +0000621b77a21d725254e928ceba9eab3dc3e14e3ebcmerge master -Dorg -Ssuccess-onlyeditome-jaieditZarrReadereditome-modeleditbio-formats-documentationeditome-stubseditome-mdbtoolseditome-poieditbioformatseditome-codecseditome-metakiteditbio-formats-examplesedit.gitmoduleseditome-common-javabioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit34a02bf417e52b422fb90ac8642aef233ec0f3c91772928298000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-08 00:04:58 +000034a02bf417e52b422fb90ac8642aef233ec0f3c9Update component versionseditome-metakiteditome-poieditbio-formats-exampleseditome-modeleditbio-formats-documentationeditbioformatseditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 8282BIOFORMATS-buildjob/BIOFORMATS-build/82789a8965cacb3244a5c92c5594e63d794a9833ea789a8965cacb3244a5c92c5594e63d794a9833eaorigin/merge_ci789a8965cacb3244a5c92c5594e63d794a9833ea789a8965cacb3244a5c92c5594e63d794a9833eaorigin/merge_ci789a8965cacb3244a5c92c5594e63d794a9833ea789a8965cacb3244a5c92c5594e63d794a9833eaorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#82133610128153BIOFORMATS-build » testintegration #8282falsefalse823277SUCCESS1772841915044https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/82/testintegration31e29afb183b95e1735a962cbaeca4b5e7c869d31772841624000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#86 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/86/) 2026-03-07 00:00:24 +000031e29afb183b95e1735a962cbaeca4b5e7c869d3merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit4b18ae49a5629d650c248f24d3870c189de8a9381772841808000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..1473abf2 Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..ec98173a19 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - 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' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#86 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/86/) 2026-03-07 00:03:28 +00004b18ae49a5629d650c248f24d3870c189de8a938merge master -Dorg -Ssuccess-onlyeditome-common-javaeditome-jaieditome-poieditome-codecseditome-stubseditbioformatseditbio-formats-exampleseditZarrReadereditbio-formats-documentationeditome-modeleditome-metakiteditome-mdbtoolsedit.gitmodulesbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit789a8965cacb3244a5c92c5594e63d794a9833ea1772841905000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-07 00:05:05 +0000789a8965cacb3244a5c92c5594e63d794a9833eaUpdate component versionseditome-modeleditbio-formats-documentationeditbio-formats-exampleseditbioformatseditome-codecseditome-poieditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 8181BIOFORMATS-buildjob/BIOFORMATS-build/813bd2a92c29dba56b572715666807f0aa12329ed23bd2a92c29dba56b572715666807f0aa12329ed2origin/merge_ci3bd2a92c29dba56b572715666807f0aa12329ed23bd2a92c29dba56b572715666807f0aa12329ed2origin/merge_ci3bd2a92c29dba56b572715666807f0aa12329ed23bd2a92c29dba56b572715666807f0aa12329ed2origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#81133861128153BIOFORMATS-build » testintegration #8181falsefalse813235SUCCESS1772755527840https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/81/testintegrationb29a5322662471b1e22a62938b95f23f37b129f81772755222000https://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#85 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/85/) 2026-03-06 00:00:22 +0000b29a5322662471b1e22a62938b95f23f37b129f8merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitfdfeade6863b9c830c0cb1cbad6f38a5048381ec1772755418000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..1473abf2 Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..ec98173a19 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - 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' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#85 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/85/) 2026-03-06 00:03:38 +0000fdfeade6863b9c830c0cb1cbad6f38a5048381ecmerge master -Dorg -Ssuccess-onlyeditome-poieditome-metakiteditbio-formats-exampleseditome-modeleditome-stubseditZarrReadereditome-mdbtoolseditome-common-javaeditbio-formats-documentationeditome-codecseditome-jaieditbioformatsedit.gitmodulesbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit3bd2a92c29dba56b572715666807f0aa12329ed21772755517000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-06 00:05:17 +00003bd2a92c29dba56b572715666807f0aa12329ed2Update component versionseditome-modeleditbio-formats-exampleseditbioformatseditome-codecseditome-metakiteditome-poieditbio-formats-documentationgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 8080BIOFORMATS-buildjob/BIOFORMATS-build/80d11e83b4755c211915b7bad899c1a078f0dfd568d11e83b4755c211915b7bad899c1a078f0dfd568origin/merge_cid11e83b4755c211915b7bad899c1a078f0dfd568d11e83b4755c211915b7bad899c1a078f0dfd568origin/merge_cid11e83b4755c211915b7bad899c1a078f0dfd568d11e83b4755c211915b7bad899c1a078f0dfd568origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#80138719128153BIOFORMATS-build » testintegration #8080falsefalse803190SUCCESS1772669120594https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/80/testintegrationeeb2dc13e4af32f9cc5add034b88253ec2d229081772668824000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#84 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/84/) 2026-03-05 00:00:24 +0000eeb2dc13e4af32f9cc5add034b88253ec2d22908merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit80be61a83610a393605941cefe1c03a19ece69ff1772669013000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..1473abf2 Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..ec98173a19 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - 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' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#84 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/84/) 2026-03-05 00:03:33 +000080be61a83610a393605941cefe1c03a19ece69ffmerge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditome-mdbtoolseditome-common-javaeditome-metakiteditZarrReadereditome-poiedit.gitmoduleseditome-jaieditome-codecseditome-stubseditome-modeleditbioformatseditbio-formats-examplesbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitd11e83b4755c211915b7bad899c1a078f0dfd5681772669111000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-05 00:05:11 +0000d11e83b4755c211915b7bad899c1a078f0dfd568Update component versionseditbio-formats-documentationeditome-metakiteditbioformatseditbio-formats-exampleseditome-modeleditome-poieditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 7979BIOFORMATS-buildjob/BIOFORMATS-build/79b681de7df1854bc7ee2430fc8d0597e745b3dee1b681de7df1854bc7ee2430fc8d0597e745b3dee1origin/merge_cib681de7df1854bc7ee2430fc8d0597e745b3dee1b681de7df1854bc7ee2430fc8d0597e745b3dee1origin/merge_cib681de7df1854bc7ee2430fc8d0597e745b3dee1b681de7df1854bc7ee2430fc8d0597e745b3dee1origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#79225572128153BIOFORMATS-build » testintegration #7979falsefalse793146SUCCESS1772582768173https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/79/testintegration7f356fbcf1e4d2a17a540f6104a18bd47130c82f1772582456000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#83 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/83/) 2026-03-04 00:00:56 +00007f356fbcf1e4d2a17a540f6104a18bd47130c82fmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit4afb0181b10eeaad3c7d4d97f50ccd20a78d0ddb1772582649000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..1473abf2 Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..ec98173a19 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - 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' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#83 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/83/) 2026-03-04 00:04:09 +00004afb0181b10eeaad3c7d4d97f50ccd20a78d0ddbmerge master -Dorg -Ssuccess-onlyeditome-poieditome-codecseditZarrReadereditbio-formats-exampleseditome-modeleditbio-formats-documentationeditbioformatseditome-common-javaeditome-jaiedit.gitmoduleseditome-mdbtoolseditome-metakiteditome-stubsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitb681de7df1854bc7ee2430fc8d0597e745b3dee11772582755000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-04 00:05:55 +0000b681de7df1854bc7ee2430fc8d0597e745b3dee1Update component versionseditome-modeleditome-poieditome-codecseditbio-formats-documentationeditbioformatseditome-metakiteditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 7878BIOFORMATS-buildjob/BIOFORMATS-build/7828c425ff9770a180a4d9eb1c3eceff3ab1920bb828c425ff9770a180a4d9eb1c3eceff3ab1920bb8origin/merge_ci28c425ff9770a180a4d9eb1c3eceff3ab1920bb828c425ff9770a180a4d9eb1c3eceff3ab1920bb8origin/merge_ci28c425ff9770a180a4d9eb1c3eceff3ab1920bb828c425ff9770a180a4d9eb1c3eceff3ab1920bb8origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#78126242128153BIOFORMATS-build » testintegration #7878falsefalse783100SUCCESS1772496330964https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/78/testintegration2595c6abd806499e036264b97afab3c35f8ba5591772496019000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#82 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/82/) 2026-03-03 00:00:19 +00002595c6abd806499e036264b97afab3c35f8ba559merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitd84e2f18b1d42680379a196731531129b546823c1772496222000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..4c66e7eb Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' - PR 458 pwalczysko 'Konica olympus' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..0db2856f26 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - 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 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#82 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/82/) 2026-03-03 00:03:42 +0000d84e2f18b1d42680379a196731531129b546823cmerge master -Dorg -Ssuccess-onlyeditome-common-javaeditbio-formats-documentationeditome-metakiteditome-mdbtoolseditome-modeleditome-stubsedit.gitmoduleseditZarrReadereditbio-formats-exampleseditome-jaieditbioformatseditome-poieditome-codecsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit28c425ff9770a180a4d9eb1c3eceff3ab1920bb81772496319000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-03 00:05:19 +000028c425ff9770a180a4d9eb1c3eceff3ab1920bb8Update component versionseditbio-formats-documentationeditome-codecseditbio-formats-exampleseditbioformatseditome-modeleditome-poieditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 7777BIOFORMATS-buildjob/BIOFORMATS-build/7754fe2bfdebf95dcb0048020ce2f8b312a46c244054fe2bfdebf95dcb0048020ce2f8b312a46c2440origin/merge_ci54fe2bfdebf95dcb0048020ce2f8b312a46c244054fe2bfdebf95dcb0048020ce2f8b312a46c2440origin/merge_ci54fe2bfdebf95dcb0048020ce2f8b312a46c244054fe2bfdebf95dcb0048020ce2f8b312a46c2440origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#77128153128153BIOFORMATS-build » testintegration #7777falsefalse773053SUCCESS1772409918896https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/77/testintegrationaf0fa7f67efd179263b7aef770a6376c70a51e101772409622000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#81 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/81/) 2026-03-02 00:00:22 +0000af0fa7f67efd179263b7aef770a6376c70a51e10merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitd8fdba490970b6d0002d339fbb9f3a26cfda18651772409813000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..4c66e7eb Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..0db2856f26 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - 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 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#81 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/81/) 2026-03-02 00:03:33 +0000d8fdba490970b6d0002d339fbb9f3a26cfda1865merge master -Dorg -Ssuccess-onlyeditome-metakiteditome-jaieditome-common-javaedit.gitmoduleseditZarrReadereditome-mdbtoolseditome-poieditome-codecseditome-stubseditbio-formats-documentationeditbio-formats-exampleseditbioformatseditome-modelbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit54fe2bfdebf95dcb0048020ce2f8b312a46c24401772409909000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-02 00:05:09 +000054fe2bfdebf95dcb0048020ce2f8b312a46c2440Update component versionseditbio-formats-exampleseditome-poieditbioformatseditome-modeleditbio-formats-documentationeditome-codecseditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 7676BIOFORMATS-buildjob/BIOFORMATS-build/760730e4716ba57f2a3c48ce401bba47963fd46dd70730e4716ba57f2a3c48ce401bba47963fd46dd7origin/merge_ci0730e4716ba57f2a3c48ce401bba47963fd46dd70730e4716ba57f2a3c48ce401bba47963fd46dd7origin/merge_ci0730e4716ba57f2a3c48ce401bba47963fd46dd70730e4716ba57f2a3c48ce401bba47963fd46dd7origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#76130478128153BIOFORMATS-build » testintegration #7676falsefalse763009SUCCESS1772323516770https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/76/testintegrationdfa33d2b5ac52577fa5d6817431f593f660e8e811772323220000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#80 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/80/) 2026-03-01 00:00:20 +0000dfa33d2b5ac52577fa5d6817431f593f660e8e81merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitd97813ca1db18002edb25408e69c5bcc96fe8c3b1772323413000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..4c66e7eb Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..0db2856f26 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - 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 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#80 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/80/) 2026-03-01 00:03:33 +0000d97813ca1db18002edb25408e69c5bcc96fe8c3bmerge master -Dorg -Ssuccess-onlyeditome-modeleditome-codecseditome-stubseditZarrReadereditbioformatseditome-poieditome-common-javaeditbio-formats-examplesedit.gitmoduleseditome-metakiteditbio-formats-documentationeditome-mdbtoolseditome-jaibioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit0730e4716ba57f2a3c48ce401bba47963fd46dd71772323509000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-03-01 00:05:09 +00000730e4716ba57f2a3c48ce401bba47963fd46dd7Update component versionseditome-poieditome-metakiteditome-modeleditbioformatseditbio-formats-exampleseditome-codecseditbio-formats-documentationgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 7575BIOFORMATS-buildjob/BIOFORMATS-build/75f0ed3181e381e92f7978baa1b3ab8b4db0826223f0ed3181e381e92f7978baa1b3ab8b4db0826223origin/merge_cif0ed3181e381e92f7978baa1b3ab8b4db0826223f0ed3181e381e92f7978baa1b3ab8b4db0826223origin/merge_cif0ed3181e381e92f7978baa1b3ab8b4db0826223f0ed3181e381e92f7978baa1b3ab8b4db0826223origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#75132879128153BIOFORMATS-build » testintegration #7575falsefalse752965SUCCESS1772237119603https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/75/testintegration006649abeedc2423f7d273f5da88761889b5519a1772236823000https://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#79 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/79/) 2026-02-28 00:00:23 +0000006649abeedc2423f7d273f5da88761889b5519amerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit6f5c12647760dfc24aeafb8ed2f44253b7ebcfc21772237014000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..4c66e7eb Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..0db2856f26 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - 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 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4419 melissalinkert 'Update to ome-common 6.2.1' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#79 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/79/) 2026-02-28 00:03:34 +00006f5c12647760dfc24aeafb8ed2f44253b7ebcfc2merge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditome-jaieditome-mdbtoolseditZarrReadereditbio-formats-exampleseditome-poieditome-modeleditome-codecsedit.gitmoduleseditome-common-javaeditome-stubseditbioformatseditome-metakitbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitf0ed3181e381e92f7978baa1b3ab8b4db08262231772237111000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-02-28 00:05:11 +0000f0ed3181e381e92f7978baa1b3ab8b4db0826223Update component versionseditbio-formats-exampleseditbioformatseditome-metakiteditome-codecseditome-modeleditbio-formats-documentationeditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 7474BIOFORMATS-buildjob/BIOFORMATS-build/741f91c919c7b61190bf67818ef9377421bb6cba101f91c919c7b61190bf67818ef9377421bb6cba10origin/merge_ci1f91c919c7b61190bf67818ef9377421bb6cba101f91c919c7b61190bf67818ef9377421bb6cba10origin/merge_ci1f91c919c7b61190bf67818ef9377421bb6cba101f91c919c7b61190bf67818ef9377421bb6cba10origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#74134156128153BIOFORMATS-build » testintegration #7474falsefalse742918SUCCESS1772150732534https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/74/testintegration3bdcd26e0774a08b6f3717d8a20d6cf88d0288b51772150421000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#78 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/78/) 2026-02-27 00:00:21 +00003bdcd26e0774a08b6f3717d8a20d6cf88d0288b5merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitb79e92418625d7c548350ccf5117331a3b5a0ab51772150623000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..4c66e7eb Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..93706309ed Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - 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 4417 melissalinkert 'VSI: recognize calibration function tag' - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..1142673 Previously merged: - 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 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' Repository: ome/ome-jai Updating e70c2ab..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#78 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/78/) 2026-02-27 00:03:43 +0000b79e92418625d7c548350ccf5117331a3b5a0ab5merge master -Dorg -Ssuccess-onlyeditome-codecseditZarrReadereditome-mdbtoolseditome-jaieditome-metakiteditbio-formats-documentationedit.gitmoduleseditbioformatseditome-poieditome-stubseditome-common-javaeditome-modeleditbio-formats-examplesbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit1f91c919c7b61190bf67818ef9377421bb6cba101772150721000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-02-27 00:05:21 +00001f91c919c7b61190bf67818ef9377421bb6cba10Update component versionseditome-codecseditbio-formats-documentationeditbio-formats-exampleseditome-poieditbioformatseditome-metakiteditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 7373BIOFORMATS-buildjob/BIOFORMATS-build/736d2f2c9c32952b344b884399af8f0aa2b955c4a16d2f2c9c32952b344b884399af8f0aa2b955c4a1origin/merge_ci6d2f2c9c32952b344b884399af8f0aa2b955c4a16d2f2c9c32952b344b884399af8f0aa2b955c4a1origin/merge_ci6d2f2c9c32952b344b884399af8f0aa2b955c4a16d2f2c9c32952b344b884399af8f0aa2b955c4a1origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#73135804128153BIOFORMATS-build » testintegration #7373falsefalse732874SUCCESS1772064338793https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/73/testintegrationde8e343f63b79ecb173b9dac570b239c157291271772064022000https://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#77 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/77/) 2026-02-26 00:00:22 +0000de8e343f63b79ecb173b9dac570b239c15729127merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit54fb734fc717e69b31c5182c4075f38bddaf5dc81772064231000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..4c66e7eb Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..306ba123d7 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4414 sbesson 'ImageReader: do not check file handle for in-memory sources' - PR 4417 melissalinkert 'VSI: recognize calibration function tag' Repository: ome/ome-codecs Updating fab1a01..1f655e6 Previously merged: - 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' Merged PRs: - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' Repository: ome/ome-common-java Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..1142673 Previously merged: - 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 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' Repository: ome/ome-jai Updating e70c2ab..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#77 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/77/) 2026-02-26 00:03:51 +000054fb734fc717e69b31c5182c4075f38bddaf5dc8merge master -Dorg -Ssuccess-onlyeditZarrReadereditome-jaieditome-metakiteditbio-formats-documentationeditome-stubseditome-mdbtoolseditome-codecseditome-poieditbio-formats-exampleseditome-modeleditbioformatsedit.gitmoduleseditome-common-javabioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit6d2f2c9c32952b344b884399af8f0aa2b955c4a11772064329000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-02-26 00:05:29 +00006d2f2c9c32952b344b884399af8f0aa2b955c4a1Update component versionseditome-codecseditbio-formats-exampleseditbioformatseditome-poieditbio-formats-documentationeditome-metakiteditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 7272BIOFORMATS-buildjob/BIOFORMATS-build/726f4f2e4919c0746a099f70be6b7147bdb63eb9f86f4f2e4919c0746a099f70be6b7147bdb63eb9f8origin/merge_ci6f4f2e4919c0746a099f70be6b7147bdb63eb9f86f4f2e4919c0746a099f70be6b7147bdb63eb9f8origin/merge_ci6f4f2e4919c0746a099f70be6b7147bdb63eb9f86f4f2e4919c0746a099f70be6b7147bdb63eb9f8origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#72231127128153BIOFORMATS-build » testintegration #7272falsefalse722830SUCCESS1771977976596https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/72/testintegrationd3502b113aaab02c8c00a0497fab47c92b8dd8b01771977655000https://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#76 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/76/) 2026-02-25 00:00:55 +0000d3502b113aaab02c8c00a0497fab47c92b8dd8b0merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitd02a90314665f555d02d46bb90fc5355caf0fcd31771977858000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..4c66e7eb Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..eddfa67065 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4414 sbesson 'ImageReader: do not check file handle for in-memory sources' - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' Repository: ome/ome-codecs Updating fab1a01..1f655e6 Previously merged: - 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' Merged PRs: - PR 45 melissalinkert 'Update to aircompressor 2.0.3' Repository: ome/ome-common-java Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..1142673 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#76 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/76/) 2026-02-25 00:04:18 +0000d02a90314665f555d02d46bb90fc5355caf0fcd3merge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditbioformatseditome-jaieditome-poieditZarrReadereditome-stubseditbio-formats-exampleseditome-modeleditome-metakiteditome-codecseditome-mdbtoolsedit.gitmoduleseditome-common-javabioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit6f4f2e4919c0746a099f70be6b7147bdb63eb9f81771977964000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-02-25 00:06:04 +00006f4f2e4919c0746a099f70be6b7147bdb63eb9f8Update component versionseditome-poieditome-metakiteditbio-formats-exampleseditome-codecseditbio-formats-documentationeditbioformatseditome-modelgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 7171BIOFORMATS-buildjob/BIOFORMATS-build/7190d17d163a0bbb48aa7930888001e1ac69fd3f3c90d17d163a0bbb48aa7930888001e1ac69fd3f3corigin/merge_ci90d17d163a0bbb48aa7930888001e1ac69fd3f3c90d17d163a0bbb48aa7930888001e1ac69fd3f3corigin/merge_ci90d17d163a0bbb48aa7930888001e1ac69fd3f3c90d17d163a0bbb48aa7930888001e1ac69fd3f3corigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#71130400128153BIOFORMATS-build » testintegration #7171falsefalse712786SUCCESS1771891522391https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/71/testintegrationb027bf78aa495f7e646951fa25cbd0981464f4491771891220000https://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#75 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/75/) 2026-02-24 00:00:20 +0000b027bf78aa495f7e646951fa25cbd0981464f449merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitbed7f82ccaad397d4e839dd39f96b224dabb415a1771891413000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..4c66e7eb Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..7fc9c2b 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..eddfa67065 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4414 sbesson 'ImageReader: do not check file handle for in-memory sources' Repository: ome/ome-codecs Updating fab1a01..1f655e6 Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..1142673 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#75 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/75/) 2026-02-24 00:03:33 +0000bed7f82ccaad397d4e839dd39f96b224dabb415amerge master -Dorg -Ssuccess-onlyeditome-jaieditbio-formats-documentationedit.gitmoduleseditome-codecseditome-common-javaeditome-poieditome-stubseditbio-formats-exampleseditbioformatseditZarrReadereditome-metakiteditome-mdbtoolseditome-modelbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit90d17d163a0bbb48aa7930888001e1ac69fd3f3c1771891512000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-02-24 00:05:12 +000090d17d163a0bbb48aa7930888001e1ac69fd3f3cUpdate component versionseditome-poieditome-codecseditbioformatseditome-metakiteditbio-formats-documentationeditome-modeleditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 7070BIOFORMATS-buildjob/BIOFORMATS-build/70d605e4f47fe907007b78166275a0734988a19a99d605e4f47fe907007b78166275a0734988a19a99origin/merge_cid605e4f47fe907007b78166275a0734988a19a99d605e4f47fe907007b78166275a0734988a19a99origin/merge_cid605e4f47fe907007b78166275a0734988a19a99d605e4f47fe907007b78166275a0734988a19a99origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#70129567128153BIOFORMATS-build » testintegration #7070falsefalse702739SUCCESS1771805120281https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/70/testintegration0fb8d8cc913654684fe7120de744434b4a74eeed1771804824000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#74 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/74/) 2026-02-23 00:00:24 +00000fb8d8cc913654684fe7120de744434b4a74eeedmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit7dbefc33fe983ee94d9985dfcb099022842209821771805016000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..4c66e7eb Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..0d488b4 Previously merged: - 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' Merged PRs: - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' Repository: openmicroscopy/bioformats Excluded PRs: - 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..eddfa67065 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4414 sbesson 'ImageReader: do not check file handle for in-memory sources' Repository: ome/ome-codecs Updating fab1a01..1f655e6 Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..1142673 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#74 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/74/) 2026-02-23 00:03:36 +00007dbefc33fe983ee94d9985dfcb09902284220982merge master -Dorg -Ssuccess-onlyeditome-poieditome-common-javaeditome-metakiteditome-stubseditome-modeledit.gitmoduleseditbio-formats-documentationeditome-codecseditome-jaieditbioformatseditZarrReadereditome-mdbtoolseditbio-formats-examplesbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitd605e4f47fe907007b78166275a0734988a19a991771805113000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-02-23 00:05:13 +0000d605e4f47fe907007b78166275a0734988a19a99Update component versionseditome-metakiteditbio-formats-exampleseditbioformatseditome-modeleditome-codecseditbio-formats-documentationeditome-poigithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 6969BIOFORMATS-buildjob/BIOFORMATS-build/693aeec156a36ecc32a5aee3778ab9f597b579c90a3aeec156a36ecc32a5aee3778ab9f597b579c90aorigin/merge_ci3aeec156a36ecc32a5aee3778ab9f597b579c90a3aeec156a36ecc32a5aee3778ab9f597b579c90aorigin/merge_ci3aeec156a36ecc32a5aee3778ab9f597b579c90a3aeec156a36ecc32a5aee3778ab9f597b579c90aorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#69128436128153BIOFORMATS-build » testintegration #6969falsefalse692695SUCCESS1771718718164https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/69/testintegrationc837e7f5e5e7b6cdfb6fc68ddd715966f7f1db531771718421000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#73 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/73/) 2026-02-22 00:00:21 +0000c837e7f5e5e7b6cdfb6fc68ddd715966f7f1db53merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit19cc531508519cd103d4f21efbe72f5d1ef361db1771718612000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..4c66e7eb Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..0d488b4 Previously merged: - 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' Merged PRs: - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' Repository: openmicroscopy/bioformats Excluded PRs: - 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..eddfa67065 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4414 sbesson 'ImageReader: do not check file handle for in-memory sources' Repository: ome/ome-codecs Updating fab1a01..1f655e6 Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..1142673 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#73 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/73/) 2026-02-22 00:03:32 +000019cc531508519cd103d4f21efbe72f5d1ef361dbmerge master -Dorg -Ssuccess-onlyeditbioformatsedit.gitmoduleseditZarrReadereditome-jaieditome-mdbtoolseditome-poieditbio-formats-exampleseditome-common-javaeditome-codecseditome-modeleditbio-formats-documentationeditome-stubseditome-metakitbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit3aeec156a36ecc32a5aee3778ab9f597b579c90a1771718709000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-02-22 00:05:09 +00003aeec156a36ecc32a5aee3778ab9f597b579c90aUpdate component versionseditbio-formats-documentationeditome-codecseditome-poieditome-modeleditome-metakiteditbio-formats-exampleseditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 6868BIOFORMATS-buildjob/BIOFORMATS-build/68ffa59270d2d44ec813c43cef823ca9d8e2858df7ffa59270d2d44ec813c43cef823ca9d8e2858df7origin/merge_ciffa59270d2d44ec813c43cef823ca9d8e2858df7ffa59270d2d44ec813c43cef823ca9d8e2858df7origin/merge_ciffa59270d2d44ec813c43cef823ca9d8e2858df7ffa59270d2d44ec813c43cef823ca9d8e2858df7origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#68131013128153BIOFORMATS-build » testintegration #6868falsefalse682682SUCCESS1771632325974https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/68/testintegration9a3df95bd8effddaee00259c30fa1465276083141771632020000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#72 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/72/) 2026-02-21 00:00:20 +00009a3df95bd8effddaee00259c30fa146527608314merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakite887f1010ef6c5dd1244c3c547054a7b7b2b78d41771632216000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..4c66e7eb Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..0d488b4 Previously merged: - 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' Merged PRs: - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' Repository: openmicroscopy/bioformats Excluded PRs: - 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..eddfa67065 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4414 sbesson 'ImageReader: do not check file handle for in-memory sources' Repository: ome/ome-codecs Updating fab1a01..1f655e6 Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..1142673 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#72 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/72/) 2026-02-21 00:03:36 +0000e887f1010ef6c5dd1244c3c547054a7b7b2b78d4merge master -Dorg -Ssuccess-onlyeditome-mdbtoolseditbioformatseditome-stubseditZarrReadereditome-common-javaeditbio-formats-exampleseditome-codecseditome-poiedit.gitmoduleseditbio-formats-documentationeditome-jaieditome-modeleditome-metakitbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitffa59270d2d44ec813c43cef823ca9d8e2858df71771632314000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-02-21 00:05:14 +0000ffa59270d2d44ec813c43cef823ca9d8e2858df7Update component versionseditome-codecseditome-metakiteditome-poieditbio-formats-documentationeditbioformatseditome-modeleditbio-formats-examplesgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 6767BIOFORMATS-buildjob/BIOFORMATS-build/67e25769e63cf509740d7ec697dc610ab57e83d609e25769e63cf509740d7ec697dc610ab57e83d609origin/merge_cie25769e63cf509740d7ec697dc610ab57e83d609e25769e63cf509740d7ec697dc610ab57e83d609origin/merge_cie25769e63cf509740d7ec697dc610ab57e83d609e25769e63cf509740d7ec697dc610ab57e83d609origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#67134778128153BIOFORMATS-build » testintegration #6767falsefalse672637SUCCESS1771545928815https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/67/testintegrationc0fd617550e37bb5a0e485abee86a3dc42fa4cef1771545622000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#71 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/71/) 2026-02-20 00:00:22 +0000c0fd617550e37bb5a0e485abee86a3dc42fa4cefmerge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit74d956fd3c5c02b2f580722d7eeaeea831879f1b1771545820000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..4c66e7eb Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..0d488b4 Previously merged: - 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' Merged PRs: - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' Repository: openmicroscopy/bioformats Excluded PRs: - 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..eddfa67065 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4414 sbesson 'ImageReader: do not check file handle for in-memory sources' Repository: ome/ome-codecs Updating fab1a01..1f655e6 Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..1142673 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#71 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/71/) 2026-02-20 00:03:40 +000074d956fd3c5c02b2f580722d7eeaeea831879f1bmerge master -Dorg -Ssuccess-onlyeditome-mdbtoolseditbio-formats-exampleseditbioformatseditome-metakiteditome-poieditome-codecseditome-stubseditome-common-javaedit.gitmoduleseditZarrReadereditome-jaieditbio-formats-documentationeditome-modelbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakite25769e63cf509740d7ec697dc610ab57e83d6091771545920000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-02-20 00:05:20 +0000e25769e63cf509740d7ec697dc610ab57e83d609Update component versionseditbio-formats-exampleseditome-metakiteditome-poieditbioformatseditome-modeleditbio-formats-documentationeditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 6666BIOFORMATS-buildjob/BIOFORMATS-build/6685283928611f308cb72cca71c1ac4784e1af45d285283928611f308cb72cca71c1ac4784e1af45d2origin/merge_ci85283928611f308cb72cca71c1ac4784e1af45d285283928611f308cb72cca71c1ac4784e1af45d2origin/merge_ci85283928611f308cb72cca71c1ac4784e1af45d285283928611f308cb72cca71c1ac4784e1af45d2origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#66140509128153BIOFORMATS-build » testintegration #6666falsefalse662593SUCCESS1771459526638https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/66/testintegratione367f652769d6e5a552b196b3b6090a6dee4c03f1771459220000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#70 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/70/) 2026-02-19 00:00:20 +0000e367f652769d6e5a552b196b3b6090a6dee4c03fmerge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit6eb1e782bb53d54c58878e3cba2cbc07f11b3d391771459419000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..4c66e7eb Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..0d488b4 Previously merged: - 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' Merged PRs: - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' Repository: openmicroscopy/bioformats Excluded PRs: - 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..eddfa67065 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4414 sbesson 'ImageReader: do not check file handle for in-memory sources' Repository: ome/ome-codecs Updating fab1a01..1f655e6 Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..1142673 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#70 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/70/) 2026-02-19 00:03:39 +00006eb1e782bb53d54c58878e3cba2cbc07f11b3d39merge master -Dorg -Ssuccess-onlyeditome-codecseditome-mdbtoolsedit.gitmoduleseditbio-formats-documentationeditome-common-javaeditome-jaieditome-poieditbioformatseditome-modeleditome-stubseditZarrReadereditbio-formats-exampleseditome-metakitbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit85283928611f308cb72cca71c1ac4784e1af45d21771459517000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-02-19 00:05:17 +000085283928611f308cb72cca71c1ac4784e1af45d2Update component versionseditbioformatseditbio-formats-documentationeditome-metakiteditome-poieditbio-formats-exampleseditome-modeleditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 6565BIOFORMATS-buildjob/BIOFORMATS-build/65960c1c613dd1f55cb7b57da29dcd7b89dd5cf6e1960c1c613dd1f55cb7b57da29dcd7b89dd5cf6e1origin/merge_ci960c1c613dd1f55cb7b57da29dcd7b89dd5cf6e1960c1c613dd1f55cb7b57da29dcd7b89dd5cf6e1origin/merge_ci960c1c613dd1f55cb7b57da29dcd7b89dd5cf6e1960c1c613dd1f55cb7b57da29dcd7b89dd5cf6e1origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#65222944128153BIOFORMATS-build » testintegration #6565falsefalse652546SUCCESS1771373164361https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/65/testintegrationad3f3958fb82b784d2be2c735d36ac5a92450b331771372849000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#69 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/69/) 2026-02-18 00:00:49 +0000ad3f3958fb82b784d2be2c735d36ac5a92450b33merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakit0657bad4c1cf035f6cf4019a3958a1266ea06b471771373048000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..4c66e7eb Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..0d488b4 Previously merged: - 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' Merged PRs: - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' Repository: openmicroscopy/bioformats Excluded PRs: - 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..eddfa67065 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' - PR 4414 sbesson 'ImageReader: do not check file handle for in-memory sources' Repository: ome/ome-codecs Updating fab1a01..1f655e6 Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..1142673 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#69 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/69/) 2026-02-18 00:04:08 +00000657bad4c1cf035f6cf4019a3958a1266ea06b47merge master -Dorg -Ssuccess-onlyeditome-modeleditome-mdbtoolseditbio-formats-documentationeditome-stubsedit.gitmoduleseditome-jaieditZarrReadereditome-poieditome-common-javaeditbio-formats-exampleseditome-metakiteditbioformatseditome-codecsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit960c1c613dd1f55cb7b57da29dcd7b89dd5cf6e11771373155000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-02-18 00:05:55 +0000960c1c613dd1f55cb7b57da29dcd7b89dd5cf6e1Update component versionseditome-codecseditbio-formats-documentationeditome-metakiteditome-modeleditbio-formats-exampleseditome-poieditbioformatsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 6464BIOFORMATS-buildjob/BIOFORMATS-build/64b79c406c55f0d9e56bed672d83aa80cc22838b85b79c406c55f0d9e56bed672d83aa80cc22838b85origin/merge_cib79c406c55f0d9e56bed672d83aa80cc22838b85b79c406c55f0d9e56bed672d83aa80cc22838b85origin/merge_cib79c406c55f0d9e56bed672d83aa80cc22838b85b79c406c55f0d9e56bed672d83aa80cc22838b85origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#64124659128153BIOFORMATS-build » testintegration #6464falsefalse642500SUCCESS1771286713686https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/64/testintegration65f03d5f71904fd0ec61c7946776cd745b1d9bc21771286422000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#68 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/68/) 2026-02-17 00:00:22 +000065f03d5f71904fd0ec61c7946776cd745b1d9bc2merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitc7760506aaa8e3f1248329101f91860a0539ab481771286604000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..4c66e7eb Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..0d488b4 Previously merged: - 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..eddfa67065 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' Repository: ome/ome-codecs Updating fab1a01..1f655e6 Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..1142673 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#68 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/68/) 2026-02-17 00:03:24 +0000c7760506aaa8e3f1248329101f91860a0539ab48merge master -Dorg -Ssuccess-onlyeditZarrReadereditome-metakiteditbio-formats-documentationeditome-mdbtoolseditome-codecseditbio-formats-exampleseditome-common-javaeditome-stubseditbioformatseditome-jaieditome-poiedit.gitmoduleseditome-modelbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitb79c406c55f0d9e56bed672d83aa80cc22838b851771286701000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-02-17 00:05:01 +0000b79c406c55f0d9e56bed672d83aa80cc22838b85Update component versionseditbio-formats-documentationeditbioformatseditome-metakiteditbio-formats-exampleseditome-modeleditome-poieditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 6363BIOFORMATS-buildjob/BIOFORMATS-build/63f2c7e74212c625008089206d772dbaaed8613118f2c7e74212c625008089206d772dbaaed8613118origin/merge_cif2c7e74212c625008089206d772dbaaed8613118f2c7e74212c625008089206d772dbaaed8613118origin/merge_cif2c7e74212c625008089206d772dbaaed8613118f2c7e74212c625008089206d772dbaaed8613118origin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#63127493128153BIOFORMATS-build » testintegration #6363falsefalse632456SUCCESS1771200306595https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/63/testintegration2428a29031c55648307695c470d52e0f2968c4d51771200019000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#67 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/67/) 2026-02-16 00:00:19 +00002428a29031c55648307695c470d52e0f2968c4d5merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakit7c1ebddb4a5f71a48cd34ec84a6e8ff2badd48dc1771200202000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..4c66e7eb Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..0d488b4 Previously merged: - 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..eddfa67065 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' Repository: ome/ome-codecs Updating fab1a01..1f655e6 Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..1142673 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#67 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/67/) 2026-02-16 00:03:22 +00007c1ebddb4a5f71a48cd34ec84a6e8ff2badd48dcmerge master -Dorg -Ssuccess-onlyeditome-metakitedit.gitmoduleseditbio-formats-documentationeditome-codecseditome-poieditbio-formats-exampleseditbioformatseditZarrReadereditome-stubseditome-modeleditome-common-javaeditome-mdbtoolseditome-jaibioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakitf2c7e74212c625008089206d772dbaaed86131181771200298000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-02-16 00:04:58 +0000f2c7e74212c625008089206d772dbaaed8613118Update component versionseditbioformatseditome-metakiteditbio-formats-exampleseditome-codecseditome-modeleditome-poieditbio-formats-documentationgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 6262BIOFORMATS-buildjob/BIOFORMATS-build/62590abc0f2e7d6c95d40c8c1b0a73432cea66f88b590abc0f2e7d6c95d40c8c1b0a73432cea66f88borigin/merge_ci590abc0f2e7d6c95d40c8c1b0a73432cea66f88b590abc0f2e7d6c95d40c8c1b0a73432cea66f88borigin/merge_ci590abc0f2e7d6c95d40c8c1b0a73432cea66f88b590abc0f2e7d6c95d40c8c1b0a73432cea66f88borigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#62128064128153BIOFORMATS-build » testintegration #6262falsefalse622412SUCCESS1771113914562https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/62/testintegration2603dab323245fa4fcea1a16e2a6064447515d391771113622000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.commerge master -Dorg -Ssuccess-only Repository: ome/bio-formats-build Already up to date. Generated by BIOFORMATS-push#66 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/66/) 2026-02-15 00:00:22 +00002603dab323245fa4fcea1a16e2a6064447515d39merge master -Dorg -Ssuccess-onlyome-common-javabioformats.gitmodulesome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationome-modelZarrReaderome-poiome-mdbtoolsome-metakitcc50184ead23bfeb94f9e08ed15c8184afc8f7581771113806000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..4c66e7eb Previously merged: - 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 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/bio-formats-examples Updating 3aa7013..0d488b4 Previously merged: - 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..eddfa67065 Previously merged: - 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 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' - PR 4362 ngladitz 'OBF: Support complex data stacks' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' Repository: ome/ome-codecs Updating fab1a01..1f655e6 Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..1142673 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#66 (https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/66/) 2026-02-15 00:03:26 +0000cc50184ead23bfeb94f9e08ed15c8184afc8f758merge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditome-common-javaeditome-metakiteditome-codecseditome-jaieditome-mdbtoolseditome-poieditome-modeleditbio-formats-exampleseditZarrReadereditbioformatseditome-stubsedit.gitmodulesbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit590abc0f2e7d6c95d40c8c1b0a73432cea66f88b1771113903000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-02-15 00:05:03 +0000590abc0f2e7d6c95d40c8c1b0a73432cea66f88bUpdate component versionseditome-modeleditome-poieditome-metakiteditbio-formats-exampleseditbioformatseditbio-formats-documentationeditome-codecsgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopblueSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 11BIOFORMATS-buildjob/BIOFORMATS-build/1125f96531abfe6c98715a85af73e754f55cab92e125f96531abfe6c98715a85af73e754f55cab92eorigin/merge_ci125f96531abfe6c98715a85af73e754f55cab92e125f96531abfe6c98715a85af73e754f55cab92eorigin/merge_ci125f96531abfe6c98715a85af73e754f55cab92e125f96531abfe6c98715a85af73e754f55cab92eorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildfalse#1316267128153BIOFORMATS-build » testintegration #11falsefalse15SUCCESS1765989374983https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/1/testintegrationgitBuild stability: No recent builds failed.icon-health-80plushealth-80plus.png100falsefalseSKIP_DOCS_VALIDATIONtrueStarted by upstream 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» testintegration #161161falsefalse1616004SUCCESS1777075528701https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/161/testintegration0d01dafbf00bb54385c03153c43cba41a3bad8f51777075222000https://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#165 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/165/) 2026-04-25 00:00:22 +00000d01dafbf00bb54385c03153c43cba41a3bad8f5merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitb1d33604ef65a52c4136580b19c2bf27b24835341777075414000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#165 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/165/) 2026-04-25 00:03:34 +0000b1d33604ef65a52c4136580b19c2bf27b2483534merge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditome-jaieditZarrReadereditome-modeleditome-common-javaeditbio-formats-exampleseditome-codecsedit.gitmoduleseditome-metakiteditome-poieditome-mdbtoolseditome-stubseditbioformatsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit7f19fb93cc859f512969e47a5ee6d5f4ba852fee1777075518000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-25 00:05:18 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161161BIOFORMATS-buildjob/BIOFORMATS-build/1617f19fb93cc859f512969e47a5ee6d5f4ba852fee7f19fb93cc859f512969e47a5ee6d5f4ba852feeorigin/merge_ci7f19fb93cc859f512969e47a5ee6d5f4ba852fee7f19fb93cc859f512969e47a5ee6d5f4ba852feeorigin/merge_ci7f19fb93cc859f512969e47a5ee6d5f4ba852fee7f19fb93cc859f512969e47a5ee6d5f4ba852feeorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildbio-formats-documentation-8.6.0-SNAPSHOT-documentation.tar.gzbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT-documentation.tar.gzbio-formats-documentation-8.6.0-SNAPSHOT-documentation.zipbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT-documentation.zipbio-formats-documentation-8.6.0-SNAPSHOT.jarbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT.jarbio-formats-examples-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bio-formats-examples/target/bio-formats-examples-8.6.0-SNAPSHOT-sources.jarbio-formats-examples-8.6.0-SNAPSHOT.jarbio-formats-build/bio-formats-examples/target/bio-formats-examples-8.6.0-SNAPSHOT.jarbio-formats_plugins-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT-sources.jarbio-formats_plugins-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT-tests.jarbio-formats_plugins-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT.jarbio-formats-tools-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT-sources.jarbio-formats-tools-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT-tests.jarbio-formats-tools-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT.jarbioformats_package-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bundles/bioformats_package/target/bioformats_package-8.6.0-SNAPSHOT.jarturbojpeg-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/forks/turbojpeg/target/turbojpeg-8.6.0-SNAPSHOT-sources.jarturbojpeg-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/forks/turbojpeg/target/turbojpeg-8.6.0-SNAPSHOT.jarformats-api-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT-sources.jarformats-api-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT-tests.jarformats-api-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT.jarformats-bsd-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT-sources.jarformats-bsd-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT-tests.jarformats-bsd-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT.jarformats-gpl-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT-sources.jarformats-gpl-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT-tests.jarformats-gpl-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT.jartest-suite-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT-sources.jartest-suite-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT-tests.jartest-suite-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT.jarome-codecs-1.1.4-SNAPSHOT-javadoc.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-javadoc.jarome-codecs-1.1.4-SNAPSHOT-sources.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-sources.jarome-codecs-1.1.4-SNAPSHOT-tests.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-tests.jarome-codecs-1.1.4-SNAPSHOT.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT.jarome-common-6.2.2-SNAPSHOT-javadoc.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-javadoc.jarome-common-6.2.2-SNAPSHOT-sources.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-sources.jarome-common-6.2.2-SNAPSHOT-tests.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-tests.jarome-common-6.2.2-SNAPSHOT.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT.jarome-jai-0.1.6-SNAPSHOT-javadoc.jarbio-formats-build/ome-jai/target/ome-jai-0.1.6-SNAPSHOT-javadoc.jarome-jai-0.1.6-SNAPSHOT-sources.jarbio-formats-build/ome-jai/target/ome-jai-0.1.6-SNAPSHO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» testintegration #161161falsefalse1616004SUCCESS1777075528701https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/161/testintegration0d01dafbf00bb54385c03153c43cba41a3bad8f51777075222000https://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#165 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/165/) 2026-04-25 00:00:22 +00000d01dafbf00bb54385c03153c43cba41a3bad8f5merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitb1d33604ef65a52c4136580b19c2bf27b24835341777075414000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#165 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/165/) 2026-04-25 00:03:34 +0000b1d33604ef65a52c4136580b19c2bf27b2483534merge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditome-jaieditZarrReadereditome-modeleditome-common-javaeditbio-formats-exampleseditome-codecsedit.gitmoduleseditome-metakiteditome-poieditome-mdbtoolseditome-stubseditbioformatsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit7f19fb93cc859f512969e47a5ee6d5f4ba852fee1777075518000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-25 00:05:18 +00007f19fb93cc859f512969e47a5ee6d5f4ba852feeUpdate component versionseditbio-formats-exampleseditbioformatseditome-codecseditome-poieditbio-formats-documentationeditome-modeleditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 161161BIOFORMATS-buildjob/BIOFORMATS-build/1617f19fb93cc859f512969e47a5ee6d5f4ba852fee7f19fb93cc859f512969e47a5ee6d5f4ba852feeorigin/merge_ci7f19fb93cc859f512969e47a5ee6d5f4ba852fee7f19fb93cc859f512969e47a5ee6d5f4ba852feeorigin/merge_ci7f19fb93cc859f512969e47a5ee6d5f4ba852fee7f19fb93cc859f512969e47a5ee6d5f4ba852feeorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildbio-formats-documentation-8.6.0-SNAPSHOT-documentation.tar.gzbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT-documentation.tar.gzbio-formats-documentation-8.6.0-SNAPSHOT-documentation.zipbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT-documentation.zipbio-formats-documentation-8.6.0-SNAPSHOT.jarbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT.jarbio-formats-examples-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bio-formats-examples/target/bio-formats-examples-8.6.0-SNAPSHOT-sources.jarbio-formats-examples-8.6.0-SNAPSHOT.jarbio-formats-build/bio-formats-examples/target/bio-formats-examples-8.6.0-SNAPSHOT.jarbio-formats_plugins-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT-sources.jarbio-formats_plugins-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT-tests.jarbio-formats_plugins-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT.jarbio-formats-tools-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT-sources.jarbio-formats-tools-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT-tests.jarbio-formats-tools-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT.jarbioformats_package-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bundles/bioformats_package/target/bioformats_package-8.6.0-SNAPSHOT.jarturbojpeg-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/forks/turbojpeg/target/turbojpeg-8.6.0-SNAPSHOT-sources.jarturbojpeg-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/forks/turbojpeg/target/turbojpeg-8.6.0-SNAPSHOT.jarformats-api-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT-sources.jarformats-api-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT-tests.jarformats-api-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT.jarformats-bsd-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT-sources.jarformats-bsd-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT-tests.jarformats-bsd-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT.jarformats-gpl-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT-sources.jarformats-gpl-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT-tests.jarformats-gpl-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT.jartest-suite-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT-sources.jartest-suite-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT-tests.jartest-suite-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT.jarome-codecs-1.1.4-SNAPSHOT-javadoc.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-javadoc.jarome-codecs-1.1.4-SNAPSHOT-sources.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-sources.jarome-codecs-1.1.4-SNAPSHOT-tests.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-tests.jarome-codecs-1.1.4-SNAPSHOT.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT.jarome-common-6.2.2-SNAPSHOT-javadoc.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-javadoc.jarome-common-6.2.2-SNAPSHOT-sources.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-sources.jarome-common-6.2.2-SNAPSHOT-tests.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-tests.jarome-common-6.2.2-SNAPSHOT.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT.jarome-jai-0.1.6-SNAPSHOT-javadoc.jarbio-formats-build/ome-jai/target/ome-jai-0.1.6-SNAPSHOT-javadoc.jarome-jai-0.1.6-SNAPSHOT-sources.jarbio-formats-build/ome-jai/target/ome-jai-0.1.6-SNAPSHO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» testintegration #161161falsefalse1616004SUCCESS1777075528701https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/161/testintegration0d01dafbf00bb54385c03153c43cba41a3bad8f51777075222000https://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#165 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/165/) 2026-04-25 00:00:22 +00000d01dafbf00bb54385c03153c43cba41a3bad8f5merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitb1d33604ef65a52c4136580b19c2bf27b24835341777075414000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#165 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/165/) 2026-04-25 00:03:34 +0000b1d33604ef65a52c4136580b19c2bf27b2483534merge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditome-jaieditZarrReadereditome-modeleditome-common-javaeditbio-formats-exampleseditome-codecsedit.gitmoduleseditome-metakiteditome-poieditome-mdbtoolseditome-stubseditbioformatsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit7f19fb93cc859f512969e47a5ee6d5f4ba852fee1777075518000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-25 00:05:18 +00007f19fb93cc859f512969e47a5ee6d5f4ba852feeUpdate component versionseditbio-formats-exampleseditbioformatseditome-codecseditome-poieditbio-formats-documentationeditome-modeleditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopSKIP_DOCS_VALIDATIONtrueStarted by upstream project "BIOFORMATS-build" build number 161161BIOFORMATS-buildjob/BIOFORMATS-build/1617f19fb93cc859f512969e47a5ee6d5f4ba852fee7f19fb93cc859f512969e47a5ee6d5f4ba852feeorigin/merge_ci7f19fb93cc859f512969e47a5ee6d5f4ba852fee7f19fb93cc859f512969e47a5ee6d5f4ba852feeorigin/merge_ci7f19fb93cc859f512969e47a5ee6d5f4ba852fee7f19fb93cc859f512969e47a5ee6d5f4ba852feeorigin/merge_cihttps://github.com/$SPACE_USER/bio-formats-buildbio-formats-documentation-8.6.0-SNAPSHOT-documentation.tar.gzbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT-documentation.tar.gzbio-formats-documentation-8.6.0-SNAPSHOT-documentation.zipbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT-documentation.zipbio-formats-documentation-8.6.0-SNAPSHOT.jarbio-formats-build/bio-formats-documentation/target/bio-formats-documentation-8.6.0-SNAPSHOT.jarbio-formats-examples-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bio-formats-examples/target/bio-formats-examples-8.6.0-SNAPSHOT-sources.jarbio-formats-examples-8.6.0-SNAPSHOT.jarbio-formats-build/bio-formats-examples/target/bio-formats-examples-8.6.0-SNAPSHOT.jarbio-formats_plugins-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT-sources.jarbio-formats_plugins-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT-tests.jarbio-formats_plugins-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bio-formats-plugins/target/bio-formats_plugins-8.6.0-SNAPSHOT.jarbio-formats-tools-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT-sources.jarbio-formats-tools-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT-tests.jarbio-formats-tools-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bio-formats-tools/target/bio-formats-tools-8.6.0-SNAPSHOT.jarbioformats_package-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/bundles/bioformats_package/target/bioformats_package-8.6.0-SNAPSHOT.jarturbojpeg-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/forks/turbojpeg/target/turbojpeg-8.6.0-SNAPSHOT-sources.jarturbojpeg-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/forks/turbojpeg/target/turbojpeg-8.6.0-SNAPSHOT.jarformats-api-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT-sources.jarformats-api-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT-tests.jarformats-api-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-api/target/formats-api-8.6.0-SNAPSHOT.jarformats-bsd-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT-sources.jarformats-bsd-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT-tests.jarformats-bsd-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-bsd/target/formats-bsd-8.6.0-SNAPSHOT.jarformats-gpl-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT-sources.jarformats-gpl-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT-tests.jarformats-gpl-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/formats-gpl/target/formats-gpl-8.6.0-SNAPSHOT.jartest-suite-8.6.0-SNAPSHOT-sources.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT-sources.jartest-suite-8.6.0-SNAPSHOT-tests.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT-tests.jartest-suite-8.6.0-SNAPSHOT.jarbio-formats-build/bioformats/components/test-suite/target/test-suite-8.6.0-SNAPSHOT.jarome-codecs-1.1.4-SNAPSHOT-javadoc.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-javadoc.jarome-codecs-1.1.4-SNAPSHOT-sources.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-sources.jarome-codecs-1.1.4-SNAPSHOT-tests.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT-tests.jarome-codecs-1.1.4-SNAPSHOT.jarbio-formats-build/ome-codecs/target/ome-codecs-1.1.4-SNAPSHOT.jarome-common-6.2.2-SNAPSHOT-javadoc.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-javadoc.jarome-common-6.2.2-SNAPSHOT-sources.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-sources.jarome-common-6.2.2-SNAPSHOT-tests.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT-tests.jarome-common-6.2.2-SNAPSHOT.jarbio-formats-build/ome-common-java/target/ome-common-6.2.2-SNAPSHOT.jarome-jai-0.1.6-SNAPSHOT-javadoc.jarbio-formats-build/ome-jai/target/ome-jai-0.1.6-SNAPSHOT-javadoc.jarome-jai-0.1.6-SNAPSHOT-sources.jarbio-formats-build/ome-jai/target/ome-jai-0.1.6-SNAPSHO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» testintegration #161161falsefalse1616004SUCCESS1777075528701https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-build/label=testintegration/161/testintegration0d01dafbf00bb54385c03153c43cba41a3bad8f51777075222000https://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#165 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/165/) 2026-04-25 00:00:22 +00000d01dafbf00bb54385c03153c43cba41a3bad8f5merge master -Dorg -Ssuccess-onlyome-common-java.gitmodulesbioformatsome-codecsome-stubsbio-formats-examplesome-jaibio-formats-documentationZarrReaderome-modelome-poiome-mdbtoolsome-metakitb1d33604ef65a52c4136580b19c2bf27b24835341777075414000https://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 Excluded PRs: - PR 113 dominikl 'Zarr v3' (stage: draft) - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 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..f04ba800 Previously merged: - 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' Conflicting PRs (not included): - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 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 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) - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) Updating 3f70394503..4fe6b0d71e Previously merged: - 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 4362 ngladitz 'OBF: Support complex data stacks' - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' Repository: ome/ome-codecs Updating fab1a01..b938c4f Previously merged: - 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 Excluded PRs: - PR 109 dominikl 'Remove jackson dependency' (stage: draft) - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..70a35d7 Previously merged: - 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..9f1b4ef Previously merged: - 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..9c3c3e2 Previously merged: - PR 14 sbesson 'Update publication system to use Central Portal' Repository: ome/ome-metakit Updating 1ba6cf1..55abb77 Previously merged: - 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 32 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' Repository: ome/ome-model Updating 3d70a1f9..142fd2ec Previously merged: - 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..d727828 Previously merged: - 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..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal' Generated by BIOFORMATS-push#165 (https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-push/165/) 2026-04-25 00:03:34 +0000b1d33604ef65a52c4136580b19c2bf27b2483534merge master -Dorg -Ssuccess-onlyeditbio-formats-documentationeditome-jaieditZarrReadereditome-modeleditome-common-javaeditbio-formats-exampleseditome-codecsedit.gitmoduleseditome-metakiteditome-poieditome-mdbtoolseditome-stubseditbioformatsbioformatsome-codecsbio-formats-examplesbio-formats-documentationome-modelome-poiome-metakit7f19fb93cc859f512969e47a5ee6d5f4ba852fee1777075518000https://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecopsnoopycrimecop@gmail.comUpdate component versions 2026-04-25 00:05:18 +00007f19fb93cc859f512969e47a5ee6d5f4ba852feeUpdate component versionseditbio-formats-exampleseditbioformatseditome-codecseditome-poieditbio-formats-documentationeditome-modeleditome-metakitgithttps://merge-ci.openmicroscopy.org/jenkins/user/snoopycrimecopsnoopycrimecop162falsefalsehudson.plugins.git.GitSCM--ffdefault