Release of Bio-Formats 6.13.0

Today we are releasing Bio-Formats 6.13.0 with a number of significant changes including a number of dependency updates and a significant number of format fixes. We have also made some API additions, allowing users to configure a fill color for undefined pixels as well as the option to preserve the original creator tag when writing OME-TIFF and OME-XML. The JPEGCodec has also been updated to allow the JPEG quality to be configured using the existing CodecOptions. A special thanks as always to the external contributors who have helped make this release happen.

The full list of changes included in this release are as follows:

File format fixes and improvements:

• Aperio SVS
  • removed broken special case path when there is only one (pyramidal) image (thanks to Alexandr Virodov)
• Bio-Rad Gel
  • fixed pixel data offsets for cropped images
• cellSens VSI
  • improved tile decoding to fail faster on invalid tiles
• CellWorX/MetaXpress
  • fixed a bug when retrieving channel metadata when the files for the entire first field are missing
• CV7000
  • extra folders mixed in with the plate data will now be ignored
  • corrected channel indexing if a subset of channels was acquired
• Lambert Instruments FLIM
  • added support for Fli 2.0 (thanks to Shaquille Louisa - Lambert Instruments)
• MetaMorph
  • prevented an exception when attempting to read metadata keys that don’t exist
• MetaMorph TIFF
  • fixed a NullPointerException when there are missing stage positions
• MRC
  • the IMOD flag is now used to determine int8 or uint8 pixel type
• NIFTI
  • improved the performance for gzip-compressed files by reducing the number of backwards seeks
• Nikon ND2
  • fixed an exception when reading blocks greater than 2GB
• OME-TIFF
  • file paths are now normalized rather than resolving symlinks
• Perkin Elmer Operetta
  • fixed series validation for single plane images (thanks to Alex Herbert)
• Zeiss CZI
  • improved the tile stitching when a pyramid does not exist

Bio-Formats improvements:

• added a new writer option preserve_creator for OME-TIFF and OME-XML writers. When set to true the original OME/Creator attribute will be preserved by the writer. If set to false, the OME Creator attribute will be updated to include the current Bio-Formats version. Attribute is set to false by default.
• enabled the configuration of the fill value for undefined pixel values through new API additions to IFormatReader. Two new methods (along with default implementations) have been added for setFillColor(Byte color) and Byte getFillColor(), the default value if undefined is 0.
• added a new -fill option to the command line tools, allowing a byte value to be configured for use with undefined pixels (0-255)
• enabled the configuration of JPEG quality in the JPEGCodec using the existing quality setting on CodecOptions (thanks to Peter Haub)
• improved JPEG performance by using in-memory cache in JPEGCodec (thanks to Pete Bankhead)
• made minor API updates to Memoizer to allow a null reader to be specified in the constructors, in which case a new ImageReader will be wrapped
• prevented file leaks in FileStitcher by closing readers when setting the class list
• fixed exceptions in FileStitcher when a no-op file pattern is encountered
• updated GitHub Actions release process

Documentation improvements:

• updated the format page for MRC to clarify list of developers and add links to latest specifications
• added new developer documentation pages for Bioconductor RBioFormats
• corrected one of the examples in the OME-TIFF specification page (thanks to Tom Boissonnet)
• updated the list of writer options to add documentation for new preserve_creator options
• updated the list of command line tools options to add documentation for new fill option
• version history and bug reporting are now linked from the main documentation page
• fixed a number of broken links
• updated the Li-Flim format page to add supported versions

Component updates:

• ome-common was upgraded to 6.0.16
• ome-model was upgraded to 6.3.3
• ome-codecs was upgraded to 0.4.5
• imagej1 was upgraded to 1.54c
• json was upgraded to 20230227
• kryo was upgraded to 5.4.0
• snakeyaml was upgraded to 2.0
• joda-time was upgraded to 2.12.2
• guava was upgraded to 31.1-jre
• jackson-annotations was upgraded to 12.14.2
• jackson-databind was upgraded to 12.14.2