v8.2.0

What's Changed

• Force isThisType check for .arf files by @melissalinkert in #4286
• Fix a bunch of Implicit type narrowing warnings by @melissalinkert in #4288
• bfopen: fix array allocations by @melissalinkert in #4291
• MIAS: fix a few sorting issues by @melissalinkert in #4301
• Document time parsing and warn if time in milliseconds is out of range by @melissalinkert in #4292
• Address CVE-2023-32697 by @ctrueden in #4295
• Fix Unidata repository URLs by @melissalinkert in #4303
• Add frameFooterBytes to image stride for DCIMG >=0x1000000 by @zacsimile in #4298
• Added Multi-Page TIFF Support for Prairie Technologies TIFFs by @foxmja in #4299
• Olympus ScanR: check getCurrentFile is the first value of getUsedFiles by @sbesson in #4302
• Remove unnecessary Python script for bumping component versions by @sbesson in #4293
• Add reader for Molecular Devices JDCE by @melissalinkert in #4305
• Leica LIF: map offsets to images by memory block ID by @melissalinkert in #4304
• ImageJ export plugin: add some checks to prevent file appending by @melissalinkert in #4289
• fix for garbled images with CZIs by @ptahmose in #4284
• Review declaration of Maven Scijava as a repository by @sbesson in #4311

New Contributors

• @foxmja made their first contribution in #4299
• @ptahmose made their first contribution in #4284

Full Changelog: v8.1.1...v8.2.0

v8.1.1

What's Changed

• Unused languages cleanup by @sbesson in #4275
• Metamorph: prevent NumberFormatException when trying to read wavelength in nm by @melissalinkert in #4274
• Make type cast explicit when calculating image count by @melissalinkert in #4277
• ND2: preserve pixel type when a multi-position dataset is found by @melissalinkert in #4276
• InCell: allow mix of 2D and 3D channels to be treated as a Z stack by @melissalinkert in #4270
• Override getAvailableOptions() in CV7000 and SVS readers by @melissalinkert in #4279
• ImspectorReader: fix NumberFormatException on setId() by @sbesson in #4282
• InCell: only record per-timepoint channel counts if timelapse enabled by @melissalinkert in #4283
• ScanR: populate exposure times even if field positions are missing by @melissalinkert in #4280
• Add CodeQL workflow by @sbesson in #4278
• FakeReader: add support for populating channel wavelengths and instrument by @sbesson in #4272

Full Changelog: v8.1.0...v8.1.1

v8.1.0

What's Changed

• Leica TCS: make sure XML file is on used files list by @melissalinkert in #4252
• Imaris Reader: support for LZ4 compression and performance improvements by @marcobitplane in #4249
• Bump ome-codecs to version 1.1.0 by @sbesson in #4257
• tiffcomment: fix -version, -no-upgrade, -debug, -trace by @melissalinkert in #4258
• bfsave: use the metadata endianness to create the byte array by @sbesson in #4261
• Add Hamamatsu DCIMG Reader by @zacsimile in #4255
• Bump logback version to 1.3.15 by @sbesson in #4263
• OIR: parse time step from TIMELAPSE axis when possible by @melissalinkert in #4259
• Bump ome-common, ome-model and ome-metakit to their latest releases by @sbesson in #4265
• FujiReader: ensure getCurrentFile is the first element of the used files list by @sbesson in #4267
• CellSensReader: set the VSI file as the first of getUsedFiles by @sbesson in #4266
• Remove outdated entry from plugins.config by @tferr in #4268

New Contributors

• @marcobitplane made their first contribution in #4249
• @tferr made their first contribution in #4268

Full Changelog: v8.0.1...v8.1.0

v8.0.1

What's Changed

• ImageInfo: only call System.exit in batch mode by @sbesson in #4250
• Operetta reader: don't add directories to the used files list by @melissalinkert in #4248
• testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list by @sbesson in #4172
• Operetta/Phenix: calculate physical Z size in micrometers by @melissalinkert in #4253
• ImageJ exporter: save original metadata by @melissalinkert in #4219

Full Changelog: v8.0.0...v8.0.1

v8.0.0

What's Changed

• Bump version to 8.0.0-SNAPSHOT by @dgault in #4208
• CV7000/8000: fix used files list when TIFFs are in a subdirectory by @melissalinkert in #4203
• Add support for reading compressed NDPI tiles by @melissalinkert in #4181
• Fix incorrect logical operators in Zeiss LSM and OME-XML readers by @sbesson in #4214
• Extend precompressed support to read DICOM and write TIFF/OME-TIFF by @melissalinkert in #4190
• RCPNL: add data for objective ID 18112 by @melissalinkert in #4224
• LIF: fix offset calculation for certain datasets with multiple unstitched files by @melissalinkert in #4222
• Allow processing multiple files sequentially in a single run, with file names read from stdin. by @tstoeter in #4200
• SDT: fix NegativeArraySizeException when reading files recorded by SPCM64 9.90 by @cqian89 in #4198
• Fix float casting when autoscaling int values to byte by @melissalinkert in #4220
• OIRReader: Major performance improvement when reading a ROI within a plane by @NicoKiaru in #4205
• Fix DICOM export in ImageJ by @melissalinkert in #4215
• Reduce DICOM write time by @melissalinkert in #4164
• CV7000: handle NullPointerException when resetting allFiles in close() by @sbesson in #4234
• Handle UnknownFormatException for batch processing multiple files. by @tstoeter in #4233
• Some improvements to OME-TIFF write performance by @melissalinkert in #4242
• Upgrade cdm-core (netcdf Java) to 5.6.0 by @melissalinkert in #4245

New Contributors

• @tstoeter made their first contribution in #4200
• @cqian89 made their first contribution in #4198

Full Changelog: v7.3.1...v8.0.0

v7.3.1

What's Changed

• Bump version to 8.0.0-SNAPSHOT by @dgault in #4187
• Fix most Java 9+ deprecation warnings in bio-formats-plugins component by @melissalinkert in #4178
• Fix Java 9+ deprecation warnings in smaller components by @melissalinkert in #4179
• Fix some Java 9+ warnings in formats-bsd by @melissalinkert in #4177
• Fix Java 9+ warnings in formats-gpl component by @melissalinkert in #4182
• Fix a few string comparisons, fixes #4184 by @melissalinkert in #4188
• ICS: Fix NPE when image name is empty by @dgault in #4197
• Columbus: update to use micrometers instead of reference frame for positions by @melissalinkert in #4180
• SVS: update isThisType to reject files with a single IFD by @melissalinkert in #4202
• Imaris: Remove empty color entries for non 0 indexed colors by @dgault in #4193
• Bump version to 7.3.1 by @dgault in #4207

Full Changelog: v7.3.0...v7.3.1

v7.3.0

What's Changed

• Bump version to 8.0.0-SNAPSHOT by @dgault in #4152
• Prairie: look for "<PV" string instead of just "PV" by @melissalinkert in #4155
• OME-XML: populate original metadata table by @melissalinkert in #4157
• Update GitHub actions versions and add M1/Java 21 build by @melissalinkert in #4154
• Turn off file-leak-detector if tests are run with Java 21 by @melissalinkert in #4159
• Remove duplicate enum check and add clarifying comment by @melissalinkert in #4162
• SimplePCI: fix Z position handling by @melissalinkert in #4163
• Work-around for breaking change in CellSens 4.1 by @ed-scanlon in #4117
• Added support for ColumbusReader to import data with z stacks by @TBlackmore in #4147
• DICOM reader: better handling of nested sequences that include pixel data by @melissalinkert in #4168
• Add -quality option to bfconvert by @melissalinkert in #4171
• bfconvert: remove extra channels if -channel was used by @melissalinkert in #4173
• Bump lower level component versions prior to 7.3.0 by @dgault in #4183
• Bump ome-poi to 5.3.9 and ome-metakit to 5.3.7 by @dgault in #4185
• Bump version to 7.3.0 by @dgault in #4186

New Contributors

• @ed-scanlon made their first contribution in #4117
• @TBlackmore made their first contribution in #4147

Full Changelog: v7.2.0...v7.3.0

v7.2.0

What's Changed

• Bump version to 7.2.0-SNAPSHOT by @melissalinkert in #4129
• Imaris HDF: populate channel names by @melissalinkert in #4112
• Add test for image names when resolutions are not flattened by @melissalinkert in #4114
• TiffReader: mark order as certain if metadata is read from ImageJ tag by @sbesson in #4135
• OIR: channel order and missing pixel block fixes by @melissalinkert in #4111
• CZI: fix image naming, especially for attachments by @melissalinkert in #4141
• CZI: use alternate source for well identifiers when available by @melissalinkert in #4145
• Plugin: Update ND2 widget indexing to fix chunkmap exception by @dgault in #4146
• Don't fail on non-4:4:4 JPEG by @CGDogan in #4061
• SVS: remove thumbnails and improve label/macro detection by @melissalinkert in #4144
• JPEG: reset useLegacy flag to its original state upon close by @melissalinkert in #4148
• Issues 4150 + 4110: Consider ZSTD with pyramid levels and fix integer arithmetic scale problem by @swg08 in #4138
• Bump version to 7.2.0 by @dgault in #4151

Full Changelog: v7.1.0...v7.2.0

v7.1.0

What's Changed

• Bump version to 7.1.0-SNAPSHOT by @dgault in #4107
• Bump org.json:json from 20230227 to 20231013 in /components/formats-gpl by @dependabot in #4106
• CV7000 improvements by @melissalinkert in #4085
• Photoshop TIFF: fix plane reading with memoization by @melissalinkert in #4075
• VSI: fix uncompressed BGR data by @melissalinkert in #4076
• Revert RunTimeException when JPEGTurbo cannot be loaded by @dgault in #4115
• TiffSaver: produce valid 4-channel RGBA images by @CGDogan in #4059
• Allow reading and writing compressed tiles by @melissalinkert in #3992
• Gha update by @jburel in #4119
• Add API and DICOM-specific implementations for providing supplemental metadata during conversion by @melissalinkert in #4016
• Bump sl4j-api to 2.x by @sbesson in #3956
• Remove duplicate org.json:json dependency declaration by @sbesson in #4125
• Bump logbook version to 1.3.14 by @dgault in #4124
• Bump org.json:json from 20230227 to 20231013 in /components/formats-bsd by @dependabot in #4123
• Bump dependency versions by @dgault in #4126
• Add CodecOptions.disableChromaSubsampling by @melissalinkert in #4057
• Update version numbers to 7.1.0 by @melissalinkert in #4128

Full Changelog: v7.0.1...v7.1.0

v7.0.1

What's Changed

• Bump version to 7.0.1-SNAPSHOT by @dgault in #4063
• Leica LIF: throw a nicer exception if no images are found by @melissalinkert in #4079
• Update GitHub Actions from checkout v2 to v3 by @melissalinkert in #4096
• TIFF: throw exception on 64-bit int data by @melissalinkert in #4098
• Gatan DM3: be more defensive in parsing acquisition mode by @melissalinkert in #4070
• File header update by @sbesson in #4094
• IVision: improve version and data type checks in isThisType by @melissalinkert in #4071
• Exporter plugin: remove any extra Channel elements by @melissalinkert in #4080
• TillVision: fix some metadata parsing and .pst detection issues by @melissalinkert in #4077
• OIR: fix off-by-one in XML block reading by @melissalinkert in #4078
• Gel: check IFD count in isThisType by @melissalinkert in #4074
• NDPI: correct for potential integer overflow in stored restart marker tag by @melissalinkert in #4083
• CZI: unify channel color parsing by @melissalinkert in #4088
• Ventana: fix tile arithmetic for smallest resolutions by @melissalinkert in #4072
• TIFF: check IFD entry offset before seeking by @melissalinkert in #4099
• Throw error when cannot load library by @CGDogan in #4090
• Bump ome-common version to 6.0.20 by @dgault in #4101
• OME-TIFF: optionally fail fast if an invalid file is encountered by @melissalinkert in #4073
• DICOM writer: throw an exception if the provided tiles don't match the expected tile size by @melissalinkert in #4097
• SVS: fix a variety of small issues by @melissalinkert in #4081
• Bump version to 7.0.1 by @dgault in #4105

Full Changelog: v7.0.0...v7.0.1