Release of Bio-Formats 5.5.2

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David Gault (Staff) David Gault (Staff)
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Release of Bio-Formats 5.5.2

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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

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:

Thanks to all the members of the community who have contributed to the success of Bio-Formats with patches and helpful feedback.


The OME Team

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