Open Microscopy Environment

Dear All,

Today we are releasing Bio-Formats 5.3.3, a bug fix release which includes the following changes:

Bug fixes:

• ImageJ
  • fix for issue when exporting from an ImagePlus ImageJ type that represents signed data. The pixel type will now remain unchanged as will the pixel values which had previously been scaled incorrectly
• Command line tools
  • fix for java.lang.IllegalArgumentException when using bfconvert via command line with option set to only convert a single time-point, channel or Z section
• Tiff writing
  • using TiffWriter to write tiled images now supports the writing of BigTIFF datasets

File format fixes:

• Applied Precision CellWorX
  • fix to now display the correct plate name and dimensions
• NIFTI
  • a few fixes for problems with byte alignment when reading non-core metadata from NIFTI headers
• Leica LIF (thanks to Michael Goelzer)
  • added support for timestamps of LIF files created with LAS AF 3.1 or newer. In the case of a halted acquisition only non-null timestamps are stored in the OME metadata
  • the physical pixel height and width were incorrectly calculated by dividing by the number of pixels. This has now been corrected to match the official Leica LIF specification documents by dividing by the number of pixels minus one
  • for backwards compatibility an option to preserve pre-5.3.3 physical sizes has been added. This can be set either via command line tools, through the API with the loci.formats.in.DynamicMetadataOptions class, or in the Bio-Formats plugin configuration in ImageJ
• Improvision TIFF
  • channel colors are now being read and if present set correctly in image metadata
• MetaMorph
  • fix for java.lang.OutOfMemoryError exceptions when reading large Metamorph TIFF plates

Updated build system:

• version history file added to MATLAB bundle as NEWS.rst
• increased TiffWriter test coverage
• added test coverage framework for command line tools including new ImageConverterTest

Documentation improvements:

• improved documentation and new examples for using tiled writing
• updated developer documentation for use of Bio-Formats as a Maven, Gradle or Ivy dependency
• documentation for Leica LIF bug fixes and use of backward compatibility options
• fixes for a number of broken links

Full details can be found at http://www.openmicroscopy.org/site/supp ... s-new.html

The software is available at:
http://downloads.openmicroscopy.org/bio-formats/5.3.3
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:

http://www.openmicroscopy.org/site/community

Regards,

The OME Team