Release of Bio-Formats 5.9.0

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Release of Bio-Formats 5.9.0

David Gault (Staff)
Dear all,

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

File format fixes and improvements:

  *   MetaMorph
     *   fixed a NullPointerException when a stage label in 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

The software is available at:
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:


The OME Team

The University of Dundee is a registered Scottish Charity, No: SC015096

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