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<div class="">Dear all,</div>
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<div class="">Today we are releasing Bio-Formats 6.1.0. This latest release contains the completion of Phase I of OME’s work on improved support for binary vessels. In addition to the KLB format we supported in version 6.0, we have now added a BigDataViewer
reader. We hope this work is useful for the light sheet microscopy community.</div>
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We’ve also worked to improve the integration of Bio-Formats 6.1 into OMERO 5.5 (to be released Summer 2019). Finally, we’ve also reviewed and updated many of Bio-Formats dependencies to align them with the Fiji ecosystem. This includes an update of the component
netcdf library used by Bio-Formats, which should improve the experience of users working with some of the HDF5-based file formats.</div>
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<div class="">New file formats:</div>
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<li class="">BDV (Big Data Viewer)</li><ul class="">
<li class="">added a new reader for Big Data Viewer files</li></ul>
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<div class="">File format fixes and improvements:</div>
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<li class="">Applied Precision CellWorX</li><ul class="">
<li class="">improved handling of thumbnail files</li></ul>
<li class="">DeltaVision</li><ul class="">
<li class="">updated handling of rcpnl files to treat each file as a single timepoint</li></ul>
<li class="">FakeReader</li><ul class="">
<li class="">removed header key from original metadata</li></ul>
<li class="">Hamamatsu VMS</li><ul class="">
<li class="">removed header key from original metadata</li></ul>
<li class="">Hitachi S-4800</li><ul class="">
<li class="">removed header key from original metadata</li></ul>
<li class="">ICS (Image Cytometry Standard)</li><ul class="">
<li class="">fixed an issue reading .ics/.ids files written by SVI Huygens (thanks to Jan Eglinger)</li></ul>
<li class="">Imaris IMS</li><ul class="">
<li class="">fixed issues with newer files which had been failing due to older netcdf version</li></ul>
<li class="">JPEG</li><ul class="">
<li class="">improved the reading of EXIF data</li></ul>
<li class="">Lambert Instruments FLIM</li><ul class="">
<li class="">added support for packed UINT12 datatype (thanks to Johan Herz)</li></ul>
<li class="">LEO</li><ul class="">
<li class="">fixed a bug with the parsing of physical sizes</li><li class="">improved support for additional global metadata fields</li></ul>
<li class="">Olympus OIR</li><ul class="">
<li class="">fixed a bug which would show empty pixels when more than 1000 timepoints</li></ul>
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<div class="">Automated test changes:</div>
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<li class="">added additional tests for HCS/SPW datasets to ensure Plate, PlateAcquisition, Well, WellSample, and WellSample position values are configured where present</li><li class="">added a new file-leak-detector test to flag potential memory leaks</li></ul>
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<div class="">Bio-Formats API changes:</div>
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<li class="">ImageConverter as used in bfconvert command line tool is now public</li><li class="">made ImageReader more defensive against exceptions thrown when determining reader type</li><li class="">fixed an issue when performing a non-sequential write for multi-resolution TIFF files</li></ul>
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<div class="">Component changes:</div>
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<li class="">ome-common was upgraded to 6.0.3</li><li class="">perf4j was upgraded to 0.9.16</li><li class="">removed Guava dependency which will be pulled transitively from the upstream ome-common dependency</li><li class="">jhdf5 was upgraded to 14.12.6</li><li class="">metadata-extractor was upgraded to 2.11.0</li><li class="">xercesImpl version 2.8.1 was added as it is no longer a dependency of metadata-extractor</li><li class="">netcdf was upgraded to 4.6.13</li></ul>
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<div class="">Full details can be found at <a href="https://docs.openmicroscopy.org/bio-formats/6.1.0/about/whats-new.html" class="">https://docs.openmicroscopy.org/bio-formats/6.1.0/about/whats-new.html</a><br class="">
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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="">
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Any problems or comments, please use the <a href="https://forum.image.sc/tags/bio-formats" class="">Image.sc forum</a> or mailing lists:<br class="">
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<a href="http://www.openmicroscopy.org/support" class="">http://www.openmicroscopy.org/support</a><br class="">
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<div class="">Regards,<br class="">
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The OME Team</div>
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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