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<div class="">Dear all,</div>
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<div class="">Today we are releasing Bio-Formats 5.9.0 which included the following changes:</div>
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<div class="">File format fixes and improvements:</div>
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<ul class="">
<li class="">MetaMorph
<ul class="">
<li class="">fixed a NullPointerException when a stage label in not present</li><li class="">ensured that reported domain is now consistent with the existence of a Plate in OME-XML</li><li class="">fixed Metamorph RGB series channel count (thanks to Jeremy Muhlich)</li></ul>
</li><li class="">Leica LIF
<ul class="">
<li class="">improved handling of dimension order for non-RGB channels</li></ul>
</li><li class="">Imspector OBF
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<li class="">added support for FLIM datasets</li></ul>
</li><li class="">Inveon
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<li class="">updated to attempt to locate renamed data files</li></ul>
</li><li class="">Volocity
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<li class="">expanded image names to include the stack parent names</li></ul>
</li><li class="">Olympus OIR
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<li class="">added a fix for slow tag reading and a potential infinite loop</li></ul>
</li><li class="">TIFF
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<li class="">added support in TiffWriter for the writing of DEFLATE (zlib) compression</li><li class="">deprecated getIFDs() in TiffParser and added getMainIFDs() and getSubIFDs()</li></ul>
</li><li class="">Zeiss CZI
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<li class="">fixed an issue with big images when tiling is present but a pyramid is not</li></ul>
</li><li class="">Nikon NIS-Elements ND2
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<li class="">prevented integer overflow exception when reading a tile from a large image</li></ul>
</li><li class="">Amersham Biosciences Gel
<ul class="">
<li class="">prevented overflow issue when reading unsigned integer values</li></ul>
</li><li class="">Cellomics
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<li class="">fixed indexing when the field counts are variable</li></ul>
</li><li class="">Trestle
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<li class="">updated to ensure consistent ordering of used files</li></ul>
</li></ul>
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<div class="">Bug fixes and improvements:</div>
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<ul class="">
<li class="">enabled building and testing with Java 9 and 10</li><li class="">added CI testing with Java 10 on AppVeyor and Travis</li><li class="">removed Java 7 from Appveyor matrix</li><li class="">updated a number of Maven plugins to current versions</li><li class="">corrected warnings in Maven configuration in sub-components </li><li class="">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)</li><li class="">improved robustness in the detection of patterns as part of the file stitching</li><li class="">fixed a bug relating to dimension order in the Bio-Formats plugins Exporter</li><li class="">fixed download URLs in Bio-Formats command-line tools</li><li class="">updated use of 'static final' to match Oracle's recommendations and convention</li><li class="">disabled upgrade checker when running unit tests</li><li class="">added support to data repo test suite for unconfigured tests</li></ul>
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<div class="">Documentation improvements:</div>
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<ul class="">
<li class=""></li><li class="">fixed unstable links flagged by automated link checking</li><li class="">begun adding testing for breakages to memo files</li><li class="">clarified ordering expectation in getUsedFiles Javadocs</li><li class="">added documentation for dimensionOrder in bfsave with the <a href="https://docs.openmicroscopy.org/bio-formats/5.9.0/developers/matlab-dev.html" class="">MATLAB toolbox</a></li><li class="">fixed broken links in previous release notes</li><li class="">expanded documentation for command-line tools to cover undocumented <a href="https://docs.openmicroscopy.org/bio-formats/5.9.0/users/comlinetools/display.html" class="">options</a> and <a href="https://docs.openmicroscopy.org/bio-formats/5.9.0/users/comlinetools/index.html" class="">environment
variables</a></li><li class="">added a new license/copyright section to the <a href="https://docs.openmicroscopy.org/bio-formats/5.9.0/about/index.html" class="">About Bio-Formats</a> page</li><li class="">updated the public format page for the Vectra QPTIFF format
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</li></ul>
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<div class="">Full details can be found at <a href="https://docs.openmicroscopy.org/bio-formats/5.9.0/about/whats-new.html" class="">https://docs.openmicroscopy.org/bio-formats/5.9.0/about/whats-new.html</a><br class="">
<br class="">
The software is available at:<br class="">
<a href="https://www.openmicroscopy.org/bio-formats/downloads/" class="">https://www.openmicroscopy.org/bio-formats/downloads/</a><br class="">
and will shortly be available from the Java-8 update site for Fiji users.<br class="">
<br class="">
Any problems or comments, please use the OME Forums or mailing lists:<br class="">
<br class="">
<a href="http://www.openmicroscopy.org/support" class="">http://www.openmicroscopy.org/support</a><br class="">
<br class="">
<br class="">
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<div class="">Regards,<br class="">
<br class="">
The OME Team</div>
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<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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