Release of Bio-Formats 5.8.0



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
    • 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:

Full details can be found at

The software is now available from the Java-8 update site for Fiji users and is also available from


The OME Team

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