Release of Bio-Formats 6.6.0

Today we are releasing Bio-Formats 6.6.0 which includes the following changes:

New file formats:

• Tecan Spark Cyto Workspace
  • Added a new reader for Tecan Spark Cyto workspace files, provided through a collaboration between Tecan Trading and Glencoe Software

File format fixes and improvements:

• Applied Precision CellWorX / MetaXpress
  • support for CellWorX and MetaXpress has now been split into separate readers
• BD Pathway
  • plate row and column dimensions now being populated
• Bitmap
  • fixed offset calculation for files larger than 2 GB
• Cellomics
  • channel data now being parsed from companion .mdb file
  • corrected Plate/Well/Image mappings for sparse plates
  • plate size now calculated using the maximum row/column index
  • plate row and column dimensions now being populated
• Gatan Digital Micrograph DM4
  • fixed support for montages with single Z dimensions
• MetaMorph Stack
  • corrected laser indexes for multi series datasets
• MIAS (Maia Scientific)
  • plate row and column dimensions now being populated
• Nikon NIS-Elements ND2
  • fixed a null pointer exception when parsing metadata key value pairs
• Olympus ScanR
  • added functionality to handle missing wells through a new option scanr.skip_missing_wells. By default the option is set to true and missing wells are skipped
• Olympus SIS TIFF
  • corrected parsing of pixel size values (thanks to Stephan Wagner-Conrad)
  • removed trailing null byte from imageName and channelName
  • improved formatting of the image reader
• PerkinElmer Opera Flex
  • plate row and column dimensions now being populated
• PerkinElmer Operetta
  • updated metadata files logic to skip plate folders
• PNG (Portable Network Graphics)
  • fixed an issue which resulted in a hanging call to openBytes
• Zeiss CZI
  • scene number is now correctly padded and indexes begin at 1
• Zeiss LSM
  • improved handling of cached plane variables

Documentation improvements:

• added new OME-TIFF plate companion sample files
• references to image index in the API documentation have been updated to plane index
• updated various links to follow the LOCI site migration
• fixed broken Javadoc links
• removed outdated references to mailing lists

Component updates:

• ome-model was upgraded to 6.2.2
• ome-common was upgraded to 6.0.6
• Memoizer version has been incremented meaning previous memo files are invalidated and will be regenerated
• kryo dependency updated to 4.0.2
• Added new sqlite-jdbc version 3.28.0 dependency for the Tecan Spark Cyto Workspace format

Bio-Formats improvements:

• removed automatic file stitching from format reader tests
• improved stringency of ChannelName and ImageName testing
• improved reader detection for image conversion testing
• reviewed all instances of whitelist/blacklist
• introduced support for GitHub Actions
• improved handling of DynamicMetadataOptions on Windows
• introduced the ability to set metadata options using a .bfoptions file
• test-suite updated to handle new .bfoptions file