Release of Bio-Formats 6.4.0

Dear all,

Today we are releasing Bio-Formats 6.4.0 which includes the following changes:

File format fixes and improvements:

  • Applied Precision CellWorX
    • added support for multiple Z sections
  • DeltaVision
    • added and updated objective metadata based on values from softWoRx 7.2.0 (thanks to David Pinto)
  • Hamamatsu NDPI
    • added support for JPEG-XR compression
    • added full support for files larger than 4 GB
    • improved support for a number of additional metadata tags
    • the Hamamatsu NDPI reader improvements are provided via work from Glencoe Software Inc.
  • InCell
    • inverted Y coordinate in plane/field positions to correct stitching of tiles
  • PerkinElmer Vectra QPTIFF
    • plane position values will now be populated on OME-XML
  • TIFF
    • values for XPosition and YPosition in original metadata will now be more accurately stored as doubles
    • implemented a fix to prevent integer overflow when reading from a large tile greater than 2 GB
  • Ventana BIF
    • improved handling of physical sizes for pre-stitched TIFFs
  • Zeiss CZI
    • added a fix for uncompressed pixels incorrectly flagged as JPEG-XR
    • fixed a bug so that line-scans are now read correctly (thanks to Stephan Wagner-Conrad)
    • improved parsing of detector metadata

Bio-Formats tools improvements:

  • added a new nobigtiff option to bfconvert to disable automatic switching to BigTiff based upon the number of pixel bytes (TIFF files larger than 4GB). This may be useful when converting using a compression codec so that the output file size is less than 4GB
  • fixed a bug in xmlvalid tool to properly handle lowercasing of file names
  • added new bfGetPlaneAtZCT function to MATLAB toolbox to retrieve a particular plane at a ZCT coordinate (thanks to Mark Kittisopikul)
  • added a new bfTestInRange helper function to MATLAB toolbox with improved performance and error handling (thanks to Mark Kittisopikul)
  • fixed a bug when using bfconvert on multi-series files with only a single timepoint, channel or Z slice selected

Bio-Formats API updates:

  • version of jxrlib has been updated to 0.2.2
  • version of ome-codecs has been updated to 0.3.0 which includes performance upgrades for
    LZW compression (thanks to Alexander Popiel)
  • moved JPEG-XR codec and service from formats-gpl to formats-bsd component
  • TiffParser and TiffSaver have now been updated to implement Closeable
  • added a documentation note to use one IFD instance per plane with saveBytes in TiffWriter
  • FormatWriter will now create output file’s parent directory if needed
  • FakeReader now allows for DeltaT to be set in INI file
  • FakeReader now handles INI files in plates created by mkfake
  • fixed a number of deprecation warnings in various readers

Full details can be found at https://docs.openmicroscopy.org/bio-formats/6.4.0/about/whats-new.html .

The software is available from https://www.openmicroscopy.org/ and is available from the Java-8 update site for Fiji users.

Any problems or comments, please use this forum with the bio-formats tag.

Best regards,
The OME Team

10 Likes

This looks great, I suspect QuPath users will appreciate it!

I notice that bioformats_package-6.4.0.jar is still within ome.staging rather than ome.releases, so isn’t picked up by simply changing the version number in my Gradle build file.

Do I just need to be patient or are any other changes needed?

Thanks a lot to the OME team, this helps a lot!!!
Regards,
Manuel

Sorry @petebankhead, it should be there now, it somehow failed to move from staging to releases the first time.

2 Likes

Thanks @dgault, it works now!

2 posts were split to a new topic: Issues uploading NDPI files into OMERO