[ome-users] Release of Bio-Formats 6.1.1

David Gault (Staff) d.gault at dundee.ac.uk
Wed Jun 12 14:51:23 BST 2019

Dear all,

Today we are releasing Bio-Formats 6.1.1 which included the following changes:

File format fixes and improvements:

  *   DeltaVision
     *   added new lens definitions associated with rcpnl files
  *   Gatan Digital Micrograph (DM3/DM4)
     *   now parsing the Montage tag to determine if tiles are present
     *   added support for polygon ROIs scaling (thanks to Sean Warren)
  *   PerkinElmer Columbus
     *   improved handling of truncated TIFF files to return blank planes
  *   PerkinElmer Opera Flex
     *   plate barcodes are now used to improve grouping and handling of truncated files
  *   TIFF (Tagged Image File Format)
     *   improved parsing times for images stored as uncompressed contiguous strips
  *   Zeiss CZI
     *   improved plane position metadata for many CZI datasets

Automated test changes:

  *   format reader tests have been updated to handle PerkinElmer Columbus datasets with flex files

Documentation improvements:

  *   added help for missing options in bfconvert command line tool

Full details can be found at https://docs.openmicroscopy.org/bio-formats/6.1.1/about/whats-new.html

The software is available at:
and will shortly be available from the Java-8 update site for Fiji users.

The following are issues which are being considered for the next minor release 6.2.0:
- inclusion of a new reader for Mikroscan TIFF (https://github.com/openmicroscopy/bioformats/pull/3333)
- inclusion of a new reader for Ventana .bif files (https://github.com/openmicroscopy/bioformats/pull/3336)
- fix for NDPI files with empty marker tag. This was originally aimed for a patch release with the fix https://github.com/openmicroscopy/bioformats/pull/3248 but after further investigation it will require a larger fix to our JPEG Turbo Service which will mean it is suitable for a minor release.

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



The OME Team

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