Release of Bio-Formats 6.2.1

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:

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

The software is available at:

and is available from the Java-8 update site for Fiji users.

Any problems or comments, please use this forum with the bio-formats tag

Regards,

The OME Team

6 Likes

Hi OME Team and @dgault ,

With this release, I can’t read my Ventana Bif files (acquired with DP200).
I have the following error :

loci.formats.FormatException: Unsupported overlap direction: LEFT

I manually re-installed 6.1.0 (version I was using last time I experienced to open a bif file), and everything worked. (I didn’t check intermediate versions).

Nico

Hi Nico,

A dedicated reader for Ventana Bif files was added in 6.2.0, older versions will attempt to use a different reader to open the files.

Currently the new Ventana Reader supports overlap directions of RIGHT and UP. If you have a file with LEFT overlap you can upload it to https://www.openmicroscopy.org/qa2/qa/upload/ and we can try and add support for it.