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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">Dear all,</span></div>
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<span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class=""></span></p>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">Today we are releasing Bio-Formats 6.0.0 This is a major update that
includes support for the updated </span><a href="http://docs.openmicroscopy.org/latest/ome-model/ome-tiff/specification.html" style="text-decoration:none;" class=""><span style="font-size: 11pt; font-family: Arial; color: rgb(17, 85, 204); text-decoration: underline; -webkit-text-decoration-skip: none; vertical-align: baseline; white-space: pre-wrap;" class="">OME-TIFF
file format</span></a><span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">, which now supports multi-resolution tiled images (so-called pyramidal file format). For more info, see
</span><a href="http://blog.openmicroscopy.org/file-formats/community/2018/11/29/ometiffpyramid/" style="text-decoration:none;" class=""><span style="font-size: 11pt; font-family: Arial; color: rgb(17, 85, 204); text-decoration: underline; -webkit-text-decoration-skip: none; vertical-align: baseline; white-space: pre-wrap;" class="">http://blog.openmicroscopy.org/file-formats/community/2018/11/29/ometiffpyramid/</span></a><span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">.
This new version of Bio-Formats also includes support for the KLB format for light sheet microscopy.
</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">Bio-Formats API changes:</span></div>
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<span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">Java 8 is now the minimum supported version</span></p>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">Sub-resolution reading:</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added MetadataList and CoreMetadataList classes</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added a new SubResolutionFormatReader abstract class for handling pyramidal format readers</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">updated all pyramid format readers to use SubResolutionFormatReader</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">deprecated getCoreMetadataList, seriesToCoreIndex, coreIndexToSeries, getCoreIndex and setCoreIndex
in IFormatWriter</span></div>
</li></ul>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added a new IPyramidHandler interface with the resolution getter methods</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">Sub-resolution writing changes:</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">IFormatWriter now extends IPyramidHandler (breaking)</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added setResolutions and getResolutions methods to IFormatWriter (breaking)</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added examples of using the sub-resolution writing API</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">* Tiled writing API changes:</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">updated IFormatWriter to use setTileSizeX(0) and setTileSizeY(0) as a way to disable tiling
(breaking)</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">updated FormatWriter to set 0 as the default values of getTileSizeX() and getTileSizeY (breaking)</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">IFormatWriter.getCompressionTypes now returns the types for the selected writer only</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">Metadata handling:</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added getter methods to MetadataTools for retrieving OME enumerations by value</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">deprecated OME enumeration getter methods in FormatReader</span></div>
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<span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">Refactor FilePatternReader logic in a new WrappedReader abstract class</span></p>
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<span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class=""></span></p>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">New file formats:</span></div>
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<span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">KLB</span></p>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added a new reader for Keller Lab Block (KLB) files</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">CV7000</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added a new reader for Yokogawa CV7000 datasets</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">GE MicroCT</span></div>
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<span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added a new reader for GE MicroCT datasets</span></p>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">File format fixes and improvements:</span></div>
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<span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">Aperio SVS/AFI</span></p>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">removed pyramidal resolutions of mismatching pixel types</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">fixed exposure times, improved image naming of AFI datasets</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">displayed original metadata keys for each channel of AFI datasets</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added support for multiple Z sections</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">DICOM</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">improved file grouping and file-to-series mapping for multi-file datasets</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">Fake</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added support for multi-resolution test images</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">now populating WellSample positions when present using Plane data</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">Gatan Digital Micrograph</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">adjusted endianness and record byte count for long values</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">allowed ROIs to be stored in DocumentObjectList groups</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">no longer creating an empty ROI when an unsupported shape type is encountered</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">Image Pro</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added support for Image Pro Plus .ips set</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">GE InCell</span></div>
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<li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added support for parsing minimum and maximum pixel values</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">Lambert Instruments FLIM</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">fixed an integer overflow error with large files (thanks to Rolf Harkes)</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">Leica LIF</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">unified metadata parsing to use DataTools.parseDouble</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">Leica SCN</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">improved support for Versa datasets</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">Micro-Manager</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">improved handling of very large metadata.txt files</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">prevented NumberFormatException for invalid double values</span></div>
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">add support for parsing ChannelColor from metadata.txt files</span></div>
</li></ul>
<li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">Metamorph</span></div>
</li><ul style="margin-top:0pt;margin-bottom:0pt;" class="">
<li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added support for multi-dimensional .scan dataset created from Scan Slide (thanks to Jeremy
Muhlich)</span></div>
</li></ul>
<li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">MRC (Medical Research Council)</span></div>
</li><ul style="margin-top:0pt;margin-bottom:0pt;" class="">
<li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">fixed endian detection for old-style headers</span></div>
</li></ul>
<li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">Nikon ND2</span></div>
</li><ul style="margin-top:0pt;margin-bottom:0pt;" class="">
<li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">prevented integer overflow when reading chunkmaps from files larger than 2GB</span></div>
</li><li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">fixed handling of duplicate and incomplete exposure time lists</span></div>
</li><li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">fixed chunk map handling when CustomData blocks are between ImageDataSeqs</span></div>
</li></ul>
<li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">OME-TIFF</span></div>
</li><ul style="margin-top:0pt;margin-bottom:0pt;" class="">
<li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added support for reading OME-TIFF with pyramidal resolutions stored as SubIFDs</span></div>
</li><li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added support for writing OME-TIFF with pyramidal resolutions</span></div>
</li><li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added support for companion OME-TIFF filesets where TIFF does not link back to the metadata
file</span></div>
</li><li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">improved handling of missing planes in TiffData</span></div>
</li></ul>
<li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">PerkinElmer Operetta</span></div>
</li><ul style="margin-top:0pt;margin-bottom:0pt;" class="">
<li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">improved support to handle datasets generated by the Harmony software</span></div>
</li></ul>
<li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">TIFF</span></div>
</li><ul style="margin-top:0pt;margin-bottom:0pt;" class="">
<li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">split IFDs into separate series if the dimensions or pixel type mismatch</span></div>
</li><li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">restricted use case for legacy TIFF JAI reader</span></div>
</li><li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">fixed a bug with FillOrder which resulted in 0 pixel values</span></div>
</li></ul>
<li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">Zeiss CZI</span></div>
</li><ul style="margin-top:0pt;margin-bottom:0pt;" class="">
<li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">reduced duplicate original metadata when reading a pyramid file</span></div>
</li></ul>
<li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">Zeiss TIFF</span></div>
</li><ul style="margin-top:0pt;margin-bottom:0pt;" class="">
<li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added support for AVI files acquired with Keyence software</span></div>
</li></ul>
<li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">Zeiss ZVI</span></div>
</li><ul style="margin-top:0pt;margin-bottom:0pt;" class="">
<li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">reuse stream for sequential calls to openBytes on the same plane</span></div>
</li></ul>
<li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">updated all pyramidal format readers to consume SubResolutionReader</span></div>
</li><li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">updated all readers to consume MetadataTools getter to retrieve enumerations</span></div>
</li><li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">reviewed all readers and plugins to close open instances of RandomAccessInputStream</span></div>
</li><li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">fixed some deprecation warnings in a number of readers</span></div>
</li><li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:12pt;" class="">
<span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">for RGB images using ChannelSeparator all channel metadata is now copied instead of just names</span></p>
</li></ul>
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class=""></span></p>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">ImageJ plugin improvements:</span></div>
<ul style="margin-top:0pt;margin-bottom:0pt;" class="">
<li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<p dir="ltr" style="line-height:1.38;margin-top:12pt;margin-bottom:0pt;" class="">
<span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">updated the updater message in the Fiji plugin (thanks to Jan Eglinger)</span></p>
</li><li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">disabled LUT writing for any plane that has a default grayscale lookup table</span></div>
</li><li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:12pt;" class="">
<span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added macro option to always skip LUT writing</span></p>
</li></ul>
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class=""></span></p>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">MATLAB toolbox improvements:</span></div>
<ul style="margin-top:0pt;margin-bottom:0pt;" class="">
<li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<p dir="ltr" style="line-height:1.38;margin-top:12pt;margin-bottom:12pt;" class="">
<span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">improved performance of bfGetPlane by removing an unnecessary data copy (thanks to Cris Luengo)</span></p>
</li></ul>
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;" class="">
<br class="">
</p>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">Command-line tools improvements:</span></div>
<ul style="margin-top:0pt;margin-bottom:0pt;" class="">
<li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<p dir="ltr" style="line-height:1.38;margin-top:12pt;margin-bottom:0pt;" class="">
<span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">bfconvert utility</span></p>
</li><ul style="margin-top:0pt;margin-bottom:0pt;" class="">
<li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added `-no-flat` option to the command-line tools to convert files with sub-resolutions</span></div>
</li><li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added `-pyramid-scale` and `-pyramid-resolutions` options to generate sub-resolutions during
conversion</span></div>
</li><li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">removed `Plate` elements when `-series` is passed as an option</span></div>
</li><li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">extended usage to describe available formats, extensions and compressions</span></div>
</li></ul>
<li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">xmlvalid utility</span></div>
</li><ul style="margin-top:0pt;margin-bottom:0pt;" class="">
<li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added new `validate` methods to `loci.formats.tools.XMLValidate` returning the validation
status</span></div>
</li><li dir="ltr" style="list-style-type: circle; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:12pt;" class="">
<span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added a return code to `xmlvalid`</span></p>
</li></ul>
</ul>
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class=""></span></p>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">Component changes:</span></div>
<ul style="margin-top:0pt;margin-bottom:0pt;" class="">
<li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<p dir="ltr" style="line-height:1.38;margin-top:12pt;margin-bottom:0pt;" class="">
<span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">ome-common was upgraded to 6.0.0</span></p>
</li><li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">ome-codecs was upgraded to 0.2.3</span></div>
</li><li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:12pt;" class="">
<span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">ome-model was upgraded to 6.0.0</span></p>
</li></ul>
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class=""></span></p>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">Automated test changes:</span></div>
<ul style="margin-top:0pt;margin-bottom:0pt;" class="">
<li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<p dir="ltr" style="line-height:1.38;margin-top:12pt;margin-bottom:0pt;" class="">
<span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added `testng.allow-missing` property allowing to skip unconfigured filesets</span></p>
</li><li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added `testUnflattenedSaneOMEXML` to compare series count to OME-XML images count when resolution
flattening is disabled</span></div>
</li><li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added `test-equivalent` target to compare pixel data between two files</span></div>
</li><li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added support for storing resolution index and resolution count in the configuration files
used for automated testing</span></div>
</li><li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:12pt;" class="">
<span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">tests now fail when a configured file throws UnknownFormatException</span></p>
</li></ul>
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class=""></span></p>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">Documentation improvements:</span></div>
<ul style="margin-top:0pt;margin-bottom:0pt;" class="">
<li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<p dir="ltr" style="line-height:1.38;margin-top:12pt;margin-bottom:0pt;" class="">
<span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">fixed the xmlvalid documentation page (thanks to Kouichi C. Nakamura)</span></p>
</li><li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">improved the memory section of the MATLAB documentation page (thanks to Kouichi C. Nakamura)</span></div>
</li><li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">extended IFormatReader Javadocs to reflect the reader guide</span></div>
</li><li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">added reference to current Adobe TIFF specification</span></div>
</li><li dir="ltr" style="list-style-type: disc; font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre;" class="">
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:12pt;" class="">
<span style="font-size: 11pt; vertical-align: baseline; white-space: pre-wrap;" class="">switched to image.sc as the reference location for public feedback</span></p>
</li></ul>
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class=""> </span></p>
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">Full details can be found at:
</span><span style="text-decoration: underline; font-size: 11pt; font-family: Arial; color: rgb(17, 85, 204); -webkit-text-decoration-skip: none; vertical-align: baseline; white-space: pre-wrap;" class=""><a href="https://docs.openmicroscopy.org/bio-formats/6.0.0/about/whats-new.html" class="">https://docs.openmicroscopy.org/bio-formats/6.0.0/about/whats-new.html</a> </span></p>
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">The software is available at:
</span><span style="line-height: 1.38; text-decoration: underline; font-size: 11pt; font-family: Arial; color: rgb(17, 85, 204); -webkit-text-decoration-skip: none; vertical-align: baseline; white-space: pre-wrap;" class=""><span style="line-height: 1.38;" class=""><a href="https://www.openmicroscopy.org/bio-formats/downloads/" class="">https://www.openmicroscopy.org/bio-formats/downloads/</a></span>
</span><span style="font-family: Arial; font-size: 11pt; white-space: pre-wrap; line-height: 1.38;" class="">and will shortly be available from the Java-8 update site for Fiji users.</span></p>
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">Any problems or comments, please use please use the
</span><a href="https://forum.image.sc/tags/bio-formats" style="line-height: 1.38; text-decoration: none;" class=""><span style="font-size: 11pt; font-family: Arial; color: rgb(17, 85, 204); text-decoration: underline; -webkit-text-decoration-skip: none; vertical-align: baseline; white-space: pre-wrap;" class="">image.sc
forum</span></a><span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">.</span></p>
<br class="">
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class=""><br class="">
</span></div>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">Regards,</span></div>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom: 0pt;" class=""><span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class="">The OME Team</span></div>
<div class=""><span style="font-size: 11pt; font-family: Arial; vertical-align: baseline; white-space: pre-wrap;" class=""><br class="">
</span></div>
</span><br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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