Release of Bio-Formats 6.5.0

Dear all,

Today we are releasing Bio-Formats 6.5.0 which includes the following changes:

File format fixes and improvements:

  • Big Data Viewer
    • improved performance of tiled reading
  • DeltaVision
    • implemented additional sanity check to header to ensure correct panel count
  • DICOM
    • improved performance of initialization of multi-file datasets. Files spread across multiple
      directories are now handled by a DICOMDIR file that groups the dataset
  • Imspector OBF
    • added support for OBF Version 6 stacks (thanks to Nils Gladitz)
    • added support for OBF Version 4 stack flush points (thanks to Nils Gladitz)
  • MetaMorph
    • ensured dimension metadata read from tags and/or .nd file rather than allowing the underlying
      TIFF reader to treat each IFD as a series
  • MetaXpress
    • added support for single site HCS variant
  • Zeiss CZI
    • fixed the position count when only one position is present and the starting index is greater than 0
  • Various Readers
    • reviewed and updated readers to prevent potential cases of integer overflow

OME-Model updates:

  • version of OME-Model has been updated to 6.1.0
  • added support for Python 3.8 and make code-generation Python 3 only (thanks to Roger Leigh)
  • added getters and setters for OME@Creator attribute for ome.xml metadata interfaces and implementations (thanks to Nils Gladitz)
  • removed unmaintained C++ OME-XML implementation (thanks to Roger Leigh)
  • updated code-generation for building on Python 3.6, 3.7 (thanks to Roger Leigh)
  • uncapped the Sphinx version for OME-Model documentation

Documentation improvements:

  • fixed a number of broken links within the documentation
  • added a new format page for MetaXpress
  • added a reference to public OBF sample images in the format page

Full details can be found at https://docs.openmicroscopy.org/bio-formats/6.5.0/about/whats-new.html .

The software is available from https://www.openmicroscopy.org/ and is available from the Java-8 update site for Fiji users.

Any problems or comments, please use this forum with the bio-formats tag.

Best regards,
The OME Team

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