Release of Bio-Formats 8.3.0

Today we are releasing Bio-Formats 8.3.0 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:

• Zeiss XRM:
  • add support for .txm and .txrm files

File format fixes:

• LiFlim
  • cast integers to double for division accuracy
• Metamorph
  • don’t reset dimensions if the well count and series count match
  • fix the encoding used for reading the .nd file
• Metamorph TIFF
  • throw more explicit exceptions if parsing invalid TIFF
• Nikon ND2
  • add TextInfoItems to original metadata before parsing
  • change the padding for a specific condition to pad to 4 byte boundaries (thanks to Matthew Smith)
  • remove the usage of position metadata when distinguishing between T and series
• OME-TIFF
  • fix optimal tile size if an IFD is not linked to an Image
• Operetta/Harmony
  • fix case where index XML is in the parent of the image directory
• SlideBook 7
  • fix miscellaneous errors (thanks to Nicola Papp)
• Tecan Spark Cyto Workspace
  • use try-with-resources when opening SQL connection
• Ventana BIF
  • fix LEFT overlap and added Z stack support
• Zeiss CZI
  • fix LightSource population to include IDs, link LightSources to Channels, and set Attenuation
  • fix IDs and reference issues for Dichroic and Detector objects
  • use millisecond units for exposure times attached to channels

Bio-Formats improvements:

• showinf: configure logging for -omexml-only after all arguments parsed
• xmlvalid: use cached XSD schemas for offline validation
• ChannelMerger: correct number of Channels in MetadataStore
• Check modulo values in repository tests
• Add workflow to report the status of the automated repository builds

Component updates:

• commons-lang was migrated to commons-lang3 and upgraded to 3.18.0
• metakit was upgraded to 5.3.9
• ome-common was upgraded to 6.1.0
• ome-codecs was upgraded to 1.1.1
• ome-jai was upgraded to 0.1.5
• ome-mdbtools was upgraded to 5.3.4
• ome-metakit was upgraded to 5.3.9
• ome-model was upgraded to 6.5.0
• ome-poi was upgraded to 5.3.10
• ome-stubs was upgraded to 6.0.3