Release of Bio-Formats 8.4.0

Today we are releasing Bio-Formats 8.4.0 which includes a new file format as well as several fixes and improvements.

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

New file formats:

• Added support for TissueGnostics TFCYTO file format, sponsored by TissueGnostics GmbH

File format fixes:

• CellH5
  • reduce memory usage
• DCIMG
  • fix indexing over multiple files (thanks to Zach Marin)
• Evident/Olympus OIR
  • fix several issues that prevented pixel blocks from being found
• Evident/Olympus VSI
  • parse timestamps for each plane if available
• FV1000
  • fix precision of ROI coordinate calculation
• Hamamatsu NDPI
  • read emission wavelength from single NDPI files
• Leica TCS
  • remove unused detector parsing logic
• LEO
  • fix tag parsing to use iso-8859-1 encoding instead of UTF-8
• Metamorph
  • fix plane position parsing for multi-series data
• Nikon ND2
  • fix dimensions and timestamp assignment for certain multi-channel datasets
  • ignore invalid bits per pixel values when determining pixel type
  • prevent pixel types other than uint8 from being set incorrectly
  • changed the plane padding for another condition to pad to 4 byte boundaries (thanks to Matthew Smith)
• OME-XML
  • fix OriginalMetadataAnnotation parsing to allow escaped characters
• RCPNL
  • define objective metadata for lens IDs 18113 and 18114

Bio-Formats improvements:

• bfconvert
  • automatically calculate a pyramid resolution count if -pyramid-scale is used without -pyramid-resolutions
  • prevent large values of -pyramid-resolutions from producing resolutions with invalid dimensions
  • fix pyramid generation when writing a subset of planes (with -channel, -z, and/or -t)
• ImageJ plugin
  • fix modulo C (e.g. lifetime) scrollbars
• MATLAB/Octave toolbox
  • fix array sizes in bfGetPlane when using Octave
• FakeReader
  • add labelPlanes attribute to include human-readable plane indexes in each image
  • link Instrument to every Image
• Add unit tests for ChannelMerger and ChannelSeparator
• Several updates to automated repository tests to eliminate invalid test failures
• Automatically generate release notes when creating a GitHub release

Component updates:

• logback was upgraded to 1.3.16
• ome-common was upgraded to 6.1.2
• ome-codecs was upgraded to 1.1.2
• ome-metakit was upgraded to 5.3.10
• ome-model was upgraded to 6.5.1
• ome-poi was upgraded to 5.3.11
• CodeQL updated to v4