Release of Bio-Formats 6.4.0

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