Repository: openmicroscopy/bioformats Excluded PRs: - 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..588e56577c Previously merged: - 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 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' - PR 4383 melissalinkert 'Bump logback version to 1.3.16' - PR 4384 melissalinkert 'Update ome-common to 6.1.1'
Repository: ome/ome-codecs Updating fab1a01..89802d5 Previously merged: - PR 43 melissalinkert 'Update to ome-common 6.1.1' - PR 42 sbesson 'Update publication build system to use Central Portal'
Merged PRs: - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags'
Repository: ome/ome-common-java Excluded PRs: - PR 108 dominikl 'Remove S3 handling' (stage: draft) Updating 2cb0b7b..d22ba60 Previously merged: - 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 105 dominikl 'Bump jackson libs to 2.20.0'
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..bd6a55a Previously merged: - 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 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags'
Repository: ome/ome-model Updating 3d70a1f9..4c979e53 Previously merged: - 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..bcea6aa Previously merged: - PR 20 melissalinkert 'Update to ome-common 6.1.1' - PR 19 sbesson 'Update publication system to use Central Portal'
Merged PRs: - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags'
Repository: ome/ome-stubs Updating 1559997..6a87342 Previously merged: - PR 12 sbesson 'Update publication build system to use Central Portal'
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