Release of Bio-Formats 6.2.1

[David Gault (Staff)]

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Dear all,

Today we are releasing Bio-Formats 6.2.1 which includes the following changes:

File format fixes and improvements:

  *   Applied Precision CellWorX
     *   corrected plane positions for series index > 0 rather than reusing positions from the first series
  *   DeltaVision
     *   added objective info for new Applied Precision 100X/1.4 lensID
     *   updated so that date from dv file will override log file date to avoid locale-dependent dates
  *   Leica LAS AF LIF (Leica Image File Format)
     *   fixed units and indexing for tile-based plane positions
  *   TIFF
     *   fixed a potential exception in MinimalTiffReader when the TIFF is stored using very large tile/strip dimensions
  *   Zeiss CZI
     *   fixed a potential index out of bounds exception when populating positions

Codec updates:

  *   ome-codecs was upgraded to 0.2.5
  *   JPEG codec updated to reduce decompression time for 8-bit RGB images
  *   Huffman codec updated to allow the decoding tree to go all the way down to the 16-bit depth required by the standard (thanks to Aaron Avery)
  *   Lossless JPEG codec updated to provide better compliance with the LJPEG standard (thanks to Aaron Avery)

Bug fixes and improvements:

  *   bfconvert has been updated so that when the dimensions of a sub-resolution are smaller than the requested tile size then they default to the size of the sub-resolution
  *   fixed a bug in the execution of bfsave in the GNU Octave environment

Documentation improvements:

  *   added instructions for building Bio-Formats with IntelliJ IDEA
  *   corrected command-line tools documentation for the novalid and noncore options
  *   updated broken links to Barre's Medical Imaging Samples
  *   updated the imagej.net<http://imagej.net> link for Zeiss LSM toolbox plugin
  *   added links to public sample files for the following formats:
     *   Big Data Viewer<https://downloads.openmicroscopy.org/images/BDV/>
     *   CellWorX<https://downloads.openmicroscopy.org/images/CellWorX>
     *   CellH5<https://downloads.openmicroscopy.org/images/CellH5/>
     *   PerkinElmer Opera Flex<https://downloads.openmicroscopy.org/images/Flex/>
     *   Gatan DM3<https://downloads.openmicroscopy.org/images/Gatan/>
     *   Image Cytometry Standard<https://downloads.openmicroscopy.org/images/ICS/>
     *   Keller Lab Block<https://downloads.openmicroscopy.org/images/KLB/>
     *   PerkinElmer Columbus<https://downloads.openmicroscopy.org/images/PerkinElmer-Columbus/>
     *   Ventana BIF<https://downloads.openmicroscopy.org/images/Ventana/>
     *   Zeiss-CZI<https://downloads.openmicroscopy.org/images/Zeiss-CZI/>

Full details can be found at https://docs.openmicroscopy.org/bio-formats/6.2.1/about/whats-new.html

The software is available at:
https://www.openmicroscopy.org/bio-formats/downloads/
and will shortly be available from the Java-8 update site for Fiji users.

Any problems or comments, please use the Image.sc forum<https://forum.image.sc/tags/bio-formats>


Regards,

The OME Team

The University of Dundee is a registered Scottish Charity, No: SC015096