Release of Bio-Formats 5.8.2



Dear all,

This week we have released 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 from the Java-8 update site for Fiji users.

Any problems or comments, please use the OME Forums or mailing lists:


The OME Team