Release of Bio-Formats 6.12.0

Today we are releasing Bio-Formats 6.12.0 with a number of significant changes. Most notably for the developer community you will find that Bio-Formats has now been updated to fully support Java 17.

Additionally in this release there have been changes to the logging dependencies which will require action from developers who consume Bio-Formats. Bio-Formats previously included a logback dependency which is now marked as optional, this will require developers to directly declare a dependency for a SLF4J binding such as logback. For further details on the changes to the logging dependencies and links to examples please see the logging documentation page.

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

File format fixes and improvements:

• Lambert Instruments FLIM
  • added support for MSB 12 to 16 bit conversion (thanks to Shaquille Louisa - Lambert Instruments)
• Olympus cellSens VSI
  • corrected tile handling to respect tile origin metadata
  • pixel data will now only be read from ets files with the prefix frame_ (funded by a partnership between Glencoe Software and Evident Scientific)
• Perkin Elmer Operetta/Harmony
  • plates containing 32-bit TIFF files will now return blank planes
• Zeiss CZI
  • fixed pyramid dimension calculation

Bio-Formats improvements:

• implemented full Java 17 support for Bio-Formats
• logback dependencies are now optional as per the SLF4J best practices (thanks to Curtis Rueden)
  • downstream consumers must now declare the specific SLF4J binding they wish to use
• CI build matrix updated to use Java versions 8, 11 and 17
• ant tasks switched to use Maven Artifact Resolver
• fixed a bug when decompressing using the Base64Codec
• added a new ImageJ macro example to Bio-Formats examples
• FakeReader now ensures correct dimension order for RGB image
• added new unit tests for FakeReader
• fixed min/max calculation for RGB data
• artifacts from the GitHub Actions build are now uploaded and archived for 30 days
• release artifacts are now generated via GitHub Actions
• fixed a number of small issues in OME-Model (thanks to Roger Leigh)

Documentation improvements:

• migrated Bio-Formats documentation to Read the Docs
• fixed and updated a number of links in documentation
• updated OME-Model links to comply with Sphinx 5 deprecation warnings
• updated GitHub Actions set-output to comply with deprecation warnings
• updated OME-TIFF documentation to add links to new sample dataset BBBC017

Component updates:

• ome-metakit was upgraded to 5.3.5
• ome-common was upgraded to 6.0.14
• ome-codecs was upgraded to 0.4.4
• ome-model was upgraded to 6.3.2
• jackson-annotations was upgraded to 12.14.1
• jackson-databind was upgraded to 12.14.1
• aircompressor was upgraded to 0.21