Release of Bio-Formats 5.8.0

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Release of Bio-Formats 5.8.0

David Gault (Staff)
Dear all,

Today we are releasing Bio-Formats 5.8.0 which includes the following changes:

New file formats:

  *   Ionpath MIBI
     *   added a new reader to support the reading of Ionpath Multiplexed Ion Beam Imaging (MIBI) files (thanks to Rachel Finck)
  *   PerkinElmer Vectra QPTIFF
     *   added support for PerkinElmer Vectra QPTIFF files (The QPTIFF Bio-Formats reader is provided through a collaboration between PerkinElmer, Inc and Glencoe Software Inc.)

File format fixes and improvements:

  *   cellSens VSI
     *   added support for lossless JPEG compression
  *   Imspector OBF
     *   improved the parsing of OBF files with embedded OME-XML metadata (thanks to Bjoern Thiel)
  *   Leica LIF
     *   companion metadata files are now attached if present
  *   Micro-Manager
     *   fixed a bug related to the parsing of the metadata closing block
  *   NRRD (Nearly Raw Raster Data)
     *   added support for GZIP pixel stream contained within a .nrrd file
  *   Olympus OIR
     *   added support for multi-file datasets
  *   OME-TIFF
     *   when files are ungrouped the dimensions are corrected by checking the indexes for each associated TiffData
  *   PerkinElmer Operetta
     *   added support for additional metadata fields such as Instrument, Wavelength and Exposure time
  *   TIFF
     *   fixed a bug when printing IFD values of type OnDemandLongArray
     *   fixed a bug when writing tile sizes for multi-series images
  *   Zeiss CZI
     *   when Z positions are not enumerated then values are calculated from a Z step
     *   metadata for DisplaySetting will now be preserved in the original metadata table

Bug fixes and improvements:

  *   removed unused ScreenReader in preparation for migrating it to be an external reader
  *   fixed a bug with the generation of thumbnails in Bio-Formats plugins
  *   updated the Maven POM to unify component version property names
  *   tile size is now reported in the core metadata when using the showinf tool
  *   added setFilePatternIds to ImporterOptions for use with Bio-Formats plugins
  *   improved the precision of format identification for MRC, I2I, and Zeiss LSM

Documentation improvements:

  *   fixed and updated a number of external documentation links
  *   added links to public NRRD samples<>

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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