Release of Bio-Formats 5.8.0

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 Bio-Formats version history.

The software is available at archived 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.