Open Microscopy Environment

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:
http://downloads.openmicroscopy.org/bio-formats/5.5.2
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:

http://www.openmicroscopy.org/site/community

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.

Regards,

The OME Team