Release of Bio-Formats 6.7.0

Today we are releasing Bio-Formats 6.7.0. This new release contains several file format updates, and several updates to resources for using Bio-Formats. We have also moved the readers for several open community formats to the BSD-2 license.

File format fixes and improvements:

• cellSens VSI
  • corrected offset checking to prevent seeking beyond EOF
• Deltavision
  • fixed a bug which resulted in an IndexOutOfBoundsException
• Hamamatsu ndpis
  • added support for channel names from NDP Shading Data
• Nikon NIS-Elements ND2
  • improved parsing of timestamp values (thanks to Ilya Parmon)
  • improved parsing of channel names and colors
• Olympus FluoView FV1000
  • fixed a bug with the handling of filter indexes
• OME-TIFF
  • resolution annotations now removed when resolutions are flattened
  • fixed handling of filesets with BinaryOnly across multiple folders
• PerkinElmer Operetta
  • channel colors now populated using emission wavelength
• TIFF
  • added support for Deflate compressed tiles/strips with lsb2msb order
  • prioritised units from TIFF tag over those from ImageJ comment
• Zeiss CZI
  • plates will now be correctly detected
  • added a new reader option zeissczi.relative_positions which when set to true will change the PositionX and PositionY values stored in OME-XML to the pixel position instead of the absolute physical stage position
  • added a new reader option zeissczi.trim_dimensions which when set to true will use the pixel block metadata to trim XY dimensions to match those reported in ZEN

Bio-Formats improvements:

• the pattern reader now supports populating channel names from pattern tokens
• the channel filler will correctly reset bits per pixel if a lookup table is applied
• existing reader options are now registered in getAvailableOptions command
• improved performance of OME-XML validation (thanks to Nils Gladitz)
• added unit tests for the upgrade of custom attributes in OME-XML transforms

Documentation improvements:

• updated link to a 2005 publication about the OME data model
• bumped low level components logback-core and logback-classic to 1.2.0
• updated the licensing for BDV, KLB and CellH5 readers to BSD
• added documentation for additional reader options
• fixed a number of broken links

The below have been relicensed under the more permissive BSD-2 clause:

• Big Data Viewer reader
• Keller Lab Block reader
• CellH5 reader
• JHDF service
• Bio-Formats GNU Octave package
• Bio-Formats MATLAB functions

Component updates:

• ome-model was upgraded to 6.2.3
• ome-common was upgraded to 6.0.7
• ome-poi was upgraded to 5.3.4
• ome-codecs was upgraded to 0.3.1
• ome-metakit was upgraded to 5.3.3
• logback was upgraded to 1.2.0