Posted by
David Gault (Staff) on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Release-of-Bio-Formats-5-9-0-tp7588414.html
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Dear all,
Today we are releasing Bio-Formats 5.9.0 which included the following changes:
File format fixes and improvements:
* MetaMorph
* fixed a NullPointerException when a stage label in not present
* ensured that reported domain is now consistent with the existence of a Plate in OME-XML
* fixed Metamorph RGB series channel count (thanks to Jeremy Muhlich)
* Leica LIF
* improved handling of dimension order for non-RGB channels
* Imspector OBF
* added support for FLIM datasets
* Inveon
* updated to attempt to locate renamed data files
* Volocity
* expanded image names to include the stack parent names
* Olympus OIR
* added a fix for slow tag reading and a potential infinite loop
* TIFF
* added support in TiffWriter for the writing of DEFLATE (zlib) compression
* deprecated getIFDs() in TiffParser and added getMainIFDs() and getSubIFDs()
* Zeiss CZI
* fixed an issue with big images when tiling is present but a pyramid is not
* Nikon NIS-Elements ND2
* prevented integer overflow exception when reading a tile from a large image
* Amersham Biosciences Gel
* prevented overflow issue when reading unsigned integer values
* Cellomics
* fixed indexing when the field counts are variable
* Trestle
* updated to ensure consistent ordering of used files
Bug fixes and improvements:
* enabled building and testing with Java 9 and 10
* added CI testing with Java 10 on AppVeyor and Travis
* removed Java 7 from Appveyor matrix
* updated a number of Maven plugins to current versions
* corrected warnings in Maven configuration in sub-components
* added a warning to clarify the behavior when passing metadata with dimensionOrder in bfsave as part of the Bio-Formats MATLAB toolbox (thanks to Jonathan Armond)
* improved robustness in the detection of patterns as part of the file stitching
* fixed a bug relating to dimension order in the Bio-Formats plugins Exporter
* fixed download URLs in Bio-Formats command-line tools
* updated use of 'static final' to match Oracle's recommendations and convention
* disabled upgrade checker when running unit tests
* added support to data repo test suite for unconfigured tests
Documentation improvements:
*
* fixed unstable links flagged by automated link checking
* begun adding testing for breakages to memo files
* clarified ordering expectation in getUsedFiles Javadocs
* added documentation for dimensionOrder in bfsave with the MATLAB toolbox<
https://docs.openmicroscopy.org/bio-formats/5.9.0/developers/matlab-dev.html>
* fixed broken links in previous release notes
* expanded documentation for command-line tools to cover undocumented options<
https://docs.openmicroscopy.org/bio-formats/5.9.0/users/comlinetools/display.html> and environment variables<
https://docs.openmicroscopy.org/bio-formats/5.9.0/users/comlinetools/index.html>
* added a new license/copyright section to the About Bio-Formats<
https://docs.openmicroscopy.org/bio-formats/5.9.0/about/index.html> page
* updated the public format page for the Vectra QPTIFF format
Full details can be found at
https://docs.openmicroscopy.org/bio-formats/5.9.0/about/whats-new.htmlThe 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 OME Forums or mailing lists:
http://www.openmicroscopy.org/supportRegards,
The OME Team
The University of Dundee is a registered Scottish Charity, No: SC015096