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<div class="">Dear all,<br class="">
<br class="">
Today we are releasing Bio-Formats 5.6.0 which includes the following changes:</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">File format fixes and improvements:</div>
<div class="">
<ul class="">
<li class="">Zeiss CZI
<ul class="">
<li class="">added support for images from Elyra PALM system</li><li class="">prevented a potential infinite loop when a scene with a pyramid is missing</li></ul>
</li><li class="">cellSens VSI
<ul class="">
<li class="">a new option has been added to throw an exception rather than logging a warning if .ets file is missing. The option, 'cellsens.fail_on_missing_ets', can be used via the MetadataOptions API, as a parameter in the command line tools or via the Bio-Formats
configuration dialog in ImageJ</li></ul>
</li><li class="">MetaMorph Stack (STK)
<ul class="">
<li class="">fixed an error with HCS style datasets always returning the first plane regardless of the requested index</li><li class="">updated to use stage labels starting with 'Scan' to detect when a whole plate is saved in a single .stk file</li><li class="">fixed a bug for ArrayIndexOutOfBoundsException when an image contains a single Z plane</li></ul>
</li><li class="">Gatan Digital Micrograph
<ul class="">
<li class="">added support for Z stacks and ROIs</li><li class="">fixed several bugs in tag parsing</li></ul>
</li><li class="">PerkinElmer Operetta
<ul class="">
<li class="">ensure TIFF files exist before reading</li></ul>
</li><li class="">JPEG
<ul class="">
<li class="">support added for images with more than Integer.MAX_VALUE pixels</li></ul>
</li></ul>
</div>
<div class="">Bug fixes and improvements:</div>
<div class="">
<ul class="">
<li class="">JPEGTileDecoder
<ul class="">
<li class="">class now implements AutoCloseable to prevent resource leaks</li></ul>
</li><li class="">Bio-Formats Plugin
<ul class="">
<li class="">improved performance when using options to concatenate multiple series together</li></ul>
</li><li class="">TiffSaver
<ul class="">
<li class="">made performance improvements to prevent the writing of a new IFD for each tile, resulting in significant file size reductions for images with a large quantity of tiles</li></ul>
</li></ul>
</div>
<div class="">Documentation improvements:</div>
<div class="">
<ul class="">
<li class="">updated website and URL links for new <a href="http://www.openmicroscopy.org" class="">http://www.openmicroscopy.org</a> website</li><li class="">added missing <a href="https://docs.openmicroscopy.org/bio-formats/5.6.0/formats/andor-sif.html" class="">Andor SIF</a> to supported formats page</li><li class="">added a new page <a href="https://docs.openmicroscopy.org/bio-formats/5.6.0/developers/wsi.html" class="">Working with whole slide images</a> outlining the API support for pyramids/resolutions</li><li class="">fixed broken documentation links for external resources which are no longer available</li><li class="">updated the style of Sphinx documentation</li></ul>
</div>
<div class="">Component architecture changes/decoupling:</div>
<div class="">
<ul class="">
<li class="">decoupled image encoding and decoding routines to the new <a href="https://github.com/ome/ome-codecs" class="">ome/ome-codecs</a> GitHub repository and consumed as 'org.openmicroscopy:ome-codecs' artifact from Maven Central</li><li class="">removed components/forks/jai - decoupled to the new <a href="https://github.com/ome/ome-jai" class="">ome/ome-jai</a> GitHub repository and consumed as part of 'org.openmicroscopy:ome-jai' artifact from Maven Central</li><li class="">replaced components/formats-api/codecs classes with wrappers around 'org.openmicroscopy:ome-codecs'</li><li class="">replaced components/formats-bsd/codecs classes with wrappers around 'org.openmicroscopy:ome-codecs'</li></ul>
</div>
<div class="">Updated build system:</div>
<div class="">
<ul class="MailOutline">
<li class="">ant now removes the build files of the bundles during 'clean' to prevent a mix of dependencies</li></ul>
<div class=""><br class="">
</div>
</div>
</div>
<div class=""><br class="">
</div>
<div class="">Full details can be found at <a href="https://docs.openmicroscopy.org/bio-formats/5.6.0/about/whats-new.html" class="">https://docs.openmicroscopy.org/bio-formats/5.6.0/about/whats-new.html</a><br class="">
<br class="">
The software is available at:<br class="">
<a href="http://www.openmicroscopy.org/bio-formats/downloads/" class="">http://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="">
Regards,<br class="">
<br class="">
The OME Team</div>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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