Release of Bio-Formats 5.8.2

[David Gault (Staff)]

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Dear all,

Today we are releasing Bio-Formats 5.8.2 which includes the following changes:

File format fixes and improvements:

  *   JPEG
     *   large images with no restart markers now revert to using DefaultJPEGReader for improved decoding
  *   Micro-Manager
     *   when available PositionName will be parsed and used as the image name
  *   Hamamatsu ndpi
     *   updated image names to be more meaningful when resolutions are not flattened
  *   InCell 2000/6000
     *   fixed an IllegalArgumentException and improved well and field indexing
  *   AVI
     *   fixed a bug with padding for RGB images
  *   NIfTI
     *   the nDimensions field is now used to read additional dimensions when size is greater than 4
  *   PerkinElmer Opera Flex
     *   fixed a bug which resulted in an incorrect field count
  *   Zeiss CZI
     *   improved handling of files with no extension

Bug fixes and improvements:

  *   an error message is now logged by ImageReader when finding a reader for an empty file
  *   added a new protected helper method to Memoizer to check if a directory is writable
  *   improved the rounding of PlanePosition values for data repo configuration testing
  *   prevented a null pointer exception when retrieving plane exposure time using Bio-Formats ImageJ macro extensions
  *   updated MinMaxCalculator to account for unflattened multi resolution images

Documentation improvements:

  *   decoupled the Bio-Formats documentation to the new ome/bio-formats-documentation GitHub repository<https://github.com/ome/bio-formats-documentation>
  *   updated Adding format/reader documentation<https://docs.openmicroscopy.org/bio-formats/5.8.2/developers/format-documentation.html> for the new decoupled workflow
  *   improved link checking in automated builds

Full details can be found at https://docs.openmicroscopy.org/bio-formats/5.8.2/about/whats-new.html

The software is available at:
https://www.openmicroscopy.org/bio-formats/downloads/
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/support


Regards,

The OME Team

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