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<div>Dear All,</div>
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<div>Today we are releasing Bio-Formats 5.2.0. This release updates the Data Model to the June 2016 schema[1] introducing Folders and simplifying both the graphical aspects of the model and code generation, adds support for two new formats; Becker & Hickl FIFO
.spc and Princeton Instruments .spe, improves performance, and features many bug fixes. With this release Java 1.7 is now the minimum supported version.</div>
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<div>Support is improved for the following formats:</div>
<div>
<ul>
<li>CellSens VSI†
<ul>
<li>fixes for correctly reading dimensions</li></ul>
</li><li>FlowSight
<ul>
<li>fixes to infer channel count from channel names (thanks to Lee Kamentsky)</li></ul>
</li><li>Hamamatsu VMS†
<ul>
<li>fixed dimensions of full-resolution images</li></ul>
</li><li>ICS writing
<ul>
<li>fixed dimension population for split files</li></ul>
</li><li>Kodak BIP
<ul>
<li>fixed handling of CCD temperature stored in hexadecimal</li></ul>
</li><li>Leica LIF
<ul>
<li>fixed incorrect plane offsets for large multi-tile files</li></ul>
</li><li>LiFlim
<ul>
<li>fixed ExposureTime check and units usage</li></ul>
</li><li>Micro-Manager
<ul>
<li>fixed handling of large datasets saved as image stacks and split over multiple files</li><li>added user documentation for file saving options</li></ul>
</li><li>MRC and Spider
<ul>
<li>fixed format type checking</li></ul>
</li><li>Nifti
<ul>
<li>fixed planeSize to prevent crashes when loading large files (thanks to Christian Niedworok)</li><li>added support for gzipped compressed .nii.gz files (thanks to Eric Barnhill)</li><li>added public samples and updated documented supported file extensions</li></ul>
</li><li>OME-TIFF
<ul>
<li>fixed Plane population errors</li><li>fixed NullPointerException when closing reader for partial multi-file filesets</li><li>reduced buffer size for RandomAccessInputStreams to improve performance</li><li>deprecated getMetadataStoreForConversion and getMetadataStoreForDisplay methods</li></ul>
</li><li>OME-XML
<ul>
<li>fixed metadata store</li></ul>
</li><li>PicoQuant
<ul>
<li>updated reader to always buffer data</li></ul>
</li><li>PNG writing</li><li>SDT
<ul>
<li>performance improvements for loading of large files</li></ul>
</li><li>SVS
<ul>
<li>fixed NumberFormatException</li></ul>
</li><li>Tiff
<ul>
<li>fixed integer overflow to read resolutions correctly</li><li>fixed handling of tiled images with tile width less than 64[/list]</li></ul>
</li><li>Zeiss CZI
<ul>
<li>fixed timestamp indexing when multiple separate channels are present</li><li>improved slide support - slides are now detected as a complete full-resolution image (instead of each tile being a separate series) and pyramid sub-resolutions and label/overview images are also detected</li></ul>
</li><li>Zeiss LSM
<ul>
<li>fixed Plane population errors</li></ul>
</li><li>Zeiss ZVI†
<ul>
<li>reworked image ordering calculation to allow for tiles</li></ul>
</li></ul>
</div>
<div>† denotes a major breaking change to the reader (typically modification of core metadata). Code changes or re-import may be necessary in ImageJ/FIJI and OMERO.</div>
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</div>
<div>In addition, Slidebook6Reader is now completely external and fully maintained by 3i (see
<a href="http://www.openmicroscopy.org/info/slidebook">http://www.openmicroscopy.org/info/slidebook</a>).</div>
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</div>
<div>Other improvements include:</div>
<div>
<ul>
<li>ImageJ fixes
<ul>
<li>to allow reader delegation when a legacy reader is enabled but not working</li><li>to allow ROIs to be imported to the ImageJ ROI manager or added to a new overlay</li></ul>
</li><li>MATLAB fixes
<ul>
<li>improved integration with Octave (thanks to Carnë Draug)</li><li>added logging initialization</li></ul>
</li><li>Command-line tools fixes
<ul>
<li>upgrade check no longer run when passing -version</li><li>common methods refactoring</li><li>showinf improvements to preload format</li><li>tiffcomment now warns that it requires an ImageDescription tag to be present in the TIFF file</li></ul>
</li></ul>
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<div>Documentation improvements include:</div>
<div>
<ul>
<li>new Micro-Manager user documentation</li><li>clarifying status of legacy Quicktime and ND2 readers</li><li>noting that the Gatan reader does not currently support stacks</li><li>more Java examples added to the developer documentation</li><li>new units page for developers</li></ul>
</div>
<div>Developer updates include:</div>
<div>
<ul>
<li>dependency bumps for native-lib-loader and xalan</li><li>DataTools, Logging, FormatTools, Formats and ClassList API updates</li><li>added many automated tests and improved FakeReader testing framework</li><li>licensing updates for XSL transforms, specification code and xsd-fu Python code (to Simplified 2-clause BSD)</li><li>Jace C++ implementation has been decoupled and marked as legacy[2]</li><li>Bio-Formats C++ native implementation has been decoupled and is now being released as OME Files C++[3]</li></ul>
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<div>Full details of all of these changes are available on the Bio-Formats version history page -</div>
<div><a href="http://www.openmicroscopy.org/site/support/bio-formats5.2/about/whats-new.html">http://www.openmicroscopy.org/site/support/bio-formats5.2/about/whats-new.html</a></div>
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<div>Bio-Formats 5.2.0 is available to download from</div>
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<div><a href="http://downloads.openmicroscopy.org/bio-formats/5.2.0/">http://downloads.openmicroscopy.org/bio-formats/5.2.0/</a></div>
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<div>and will shortly be available for recent Fiji versions via the Java-8 update site. If you are using an older version of Fiji (pre-2016), you will need to upgrade to Java 8 and install a newer version, see </div>
<div><a href="http://imagej.net/2016-05-10_-_ImageJ_HOWTO_-_Java_8,_Java_6,_Java_3D">http://imagej.net/2016-05-10_-_ImageJ_HOWTO_-_Java_8,_Java_6,_Java_3D</a> for advice.</div>
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<div>Any problems or comments, please use the OME Forums or mailing lists:</div>
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<div><a href="http://www.openmicroscopy.org/site/community">http://www.openmicroscopy.org/site/community</a></div>
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<div>Regards,</div>
<div><br>
</div>
<div>The OME Team</div>
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<div>[1] <a href="http://www.openmicroscopy.org/site/support/ome-model/schemas/june-2016.html">
http://www.openmicroscopy.org/site/support/ome-model/schemas/june-2016.html</a></div>
<div>[2] <a href="https://github.com/ome/bio-formats-jace">https://github.com/ome/bio-formats-jace</a></div>
<div>[3] <a href="http://downloads.openmicroscopy.org/ome-files-cpp/">http://downloads.openmicroscopy.org/ome-files-cpp/</a></div>
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<div>Dr Helen Flynn</div>
<div>OME Technical Writer</div>
<div>Centre for Gene Regulation & Expression</div>
<div>Open Microscopy Environment</div>
<div>University of Dundee</div>
<div><a href="http://openmicroscopy.org">http://openmicroscopy.org</a></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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