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Release of Bio-Formats 5.5.2

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Questions can be asked under https://forum.image.sc/tags/ome

Release of Bio-Formats 5.5.2

Postby dgault » Thu Jun 15, 2017 4:06 pm

Dear all,

Today we are releasing Bio-Formats 5.5.2 which includes the following changes:

File format fixes and improvements:
  • Olympus FluoView FV1000
    • fix for java.lang.ArrayIndexOutOfBoundsException caused by filter name of "---" (thanks to Stefan Helfrich)
    • refactored channel metadata population and increased usage of DataTools utility functions
  • Zeiss CZI
    • fixed detection of Z line scans that caused incorrect dimensions in certain filesets
    • improved exception handling of truncated/invalid files
  • Veeco AFM
    • fixed reading of tiled images
  • Hamamatsu ndpi
    • prevented potential memory leak by ensuring all TiffParser streams are closed

Bug fixes:
  • OMEXMLServiceImpl
    • improved exception handling to deal with potential java.lang.NullPointerException when unable to locate OME-XML version while attempting to transform to the latest version

Documentation improvements:
  • updated documentation to be compatible with the latest version of Sphinx 1.6
  • fixed the usage/references of the option markup in documentation
  • fixed the table in the Micro-Manager user page
  • updated metadata ratings for supported formats

Updated build system:
  • OME-Model version bump
    • the ome-model component has been updated to 5.5.4 which includes improvements to performance, documentation and the C++ model implementation

Full details can be found at http://www.openmicroscopy.org/site/supp ... s-new.html

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:


Thank you to all the members of the community who contributed to the success of Bio-Formats with patches and helpful suggestions over the last year.


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