Release of Bio-Formats 6.6.0

Dear all,

Today we are releasing Bio-Formats 6.6.0 which included 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  • removed outdated references to mailing lists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

Full details can be found at https://docs.openmicroscopy.org/bio-formats/6.6.0/about/whats-new.html

The software is available at:

and should now be available from the Java-8 update site for Fiji users. Note, for FIJI users looking to use the new Tecan Spark Cyto Workspace format an additional dependency of sqlite-jdbc will be required.

Any problems or comments, please use the Image.sc forum

Regards,

The OME Team

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