Release of Bio-Formats 5.9.0

Today we are releasing Bio-Formats 5.9.0 which includes the following changes:

File format fixes and improvements:

• MetaMorph
  • fixed a NullPointerException when a stage label is not present
  • ensured that reported domain is now consistent with the existence of a Plate in OME-XML
  • fixed Metamorph RGB series channel count (thanks to Jeremy Muhlich)
• Leica LIF
  • improved handling of dimension order for non-RGB channels
• Imspector OBF
  • added support for FLIM datasets
• Inveon
  • updated to attempt to locate renamed data files
• Volocity
  • expanded image names to include the stack parent names
• Olympus OIR
  • added a fix for slow tag reading and a potential infinite loop
• TIFF
  • added support in TiffWriter for the writing of DEFLATE (zlib) compression
  • deprecated getIFDs() in TiffParser and added getMainIFDs() and getSubIFDs()
• Zeiss CZI
  • fixed an issue with big images when tiling is present but a pyramid is not
• Nikon NIS-Elements ND2
  • prevented integer overflow exception when reading a tile from a large image
• Amersham Biosciences Gel
  • prevented overflow issue when reading unsigned integer values
• Cellomics
  • fixed indexing when the field counts are variable
• Trestle
  • updated to ensure consistent ordering of used files

Bug fixes and improvements:

• enabled building and testing with Java 9 and 10
• added CI testing with Java 10 on AppVeyor and Travis
• removed Java 7 from Appveyor matrix
• updated a number of Maven plugins to current versions
• corrected warnings in Maven configuration in sub-components
• added a warning to clarify the behavior when passing metadata with dimensionOrder in bfsave as part of the Bio-Formats MATLAB toolbox (thanks to Jonathan Armond)
• improved robustness in the detection of patterns as part of the file stitching
• fixed a bug relating to dimension order in the Bio-Formats plugins Exporter
• fixed download URLs in Bio-Formats command-line tools
• updated use of static final to match Oracle’s recommendations and convention
• disabled upgrade checker when running unit tests
• added support to data repo test suite for unconfigured tests

Documentation improvements:

• fixed unstable links flagged by automated link checking
• begun adding testing for breakages to memo files
• clarified ordering expectation in getUsedFiles Javadocs
• added documentation for dimensionOrder in bfsave with the MATLAB toolbox
• fixed broken links in previous release notes
• expanded documentation for command-line tools to cover undocumented options and environment variables
• added a new license/copyright section to the About Bio-Formats page
• updated the public format page for the Vectra QPTIFF format

Full details can be found at Bio-Formats version history.

The software is available at archived downloads and will shortly be available from the Java-8 update site for Fiji users.

Any problems or comments, please use the OME Forums or mailing lists.