Release of Bio-Formats 5.8.2

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Release of Bio-Formats 5.8.2

David Gault (Staff)
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<>
  *   updated Adding format/reader documentation<> for the new decoupled workflow
  *   improved link checking in automated builds

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:


The OME Team

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