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<p>Dear Helen,</p>
<p>first of all I'd like to thank you and everyone involved very
much for bringing jpegXR to Bio-formats! I want to stress that we
appreciate your efforts a lot - we know that getting to this point
was hard work.<br>
</p>
<p> In our facility at the Biozentrum in Basel, we run an Zeiss
Axioscan Slidescanner that produces lots (!) of data. Using JpegXR
and our OMERO installation, we are one big step further in dealing
with this data in an elegant way. Thanks again!<br>
</p>
<p>Of course I could not wait to test the new BF on our datasets,
two of which I have uploaded to your servers (QA Bug | 17472).</p>
<p>Unfortunately for me these two compressed files did not open
(both exceptions can be found in the attached txt file).</p>
<p>I also have another question regarding your update:<br>
</p>
<p>
<blockquote type="cite">added two options to the CZI reader to
disable autostitching and exclude pyramid file attachments.
Added new checkboxes to the CZI configuration interface of the
ImageJ plugin to activate these options</blockquote>
</p>
<p>How can I access these options?</p>
<p>Again, many thanks and regards,</p>
<p>Kai<br>
</p>
<br>
<div class="moz-cite-prefix">On 12/12/2016 04:31 PM, Helen Flynn
(Staff) wrote:<br>
</div>
<blockquote
cite="mid:%3C97344E42-0BB4-4ECE-9E23-2192816CA52C@dundee.ac.uk%3E"
type="cite">
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Dear All,</div>
<div style="margin: 0px 0px 0.75em; line-height: 1.5em;
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Today we are releasing Bio-Formats 5.3.0 which includes the
following changes:</div>
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New features/API:</div>
<ul style="line-height: 1.5em; padding: 0px; list-style-image:
url(https://www.openmicroscopy.org/site/bullet.gif);
list-style-type: square; margin: 0.5em 0px 0px 1.5em;
font-family: 'Lucida Grande', Verdana, Lucida, Helvetica, Arial,
sans-serif; font-size: 13.02400016784668px;" class="">
<li style="margin-bottom: 0.5em;" class="">added support for
JPEG-XR compressed CZI data (funded by a partnership between
Glencoe Software and ZEISS), adding ‘ome:jxrlib’ as a new
dependency of Bio-Formats</li>
<li style="margin-bottom: 0.5em;" class="">improved tile-based
image writing
<ul style="line-height: 1.5em; padding: 0px; list-style-image:
url(https://www.openmicroscopy.org/site/bullet.gif);
list-style-type: square; margin: 0.5em 0px 0px 1.5em;"
class="">
<li style="margin-bottom: 0.5em;" class="">added new methods
to the loci.formats.IFormatWriter interface allowing to
set and retrieve the tile along the X and Y dimensions</li>
<li style="margin-bottom: 0.5em;" class="">added default
implementations to the loci.formats.FormatWriter abstract
class defaulting to the entire image width/height</li>
<li style="margin-bottom: 0.5em;" class="">added
functionality to loci.formats.TiffWriter adding support
for tiled images writing for TIFF and derived formats like
OME-TIFF</li>
<li style="margin-bottom: 0.5em;" class="">added developer
documentation and samples for tiled reading/writing</li>
</ul>
</li>
<li style="margin-bottom: 0.5em;" class="">added a new
MetadataOptions implementation supporting arbitrary key/value
pairs</li>
<li style="margin-bottom: 0.5em;" class="">updated the display
command line utility to support passing key/value options
using showinf -option</li>
<li style="margin-bottom: 0.5em;" class="">added two options to
the CZI reader to disable autostitching and exclude pyramid
file attachments. Added new checkboxes to the CZI
configuration interface of the ImageJ plugin to activate these
options</li>
</ul>
<div style="margin: 0px 0px 0.75em; line-height: 1.5em;
font-family: 'Lucida Grande', Verdana, Lucida, Helvetica, Arial,
sans-serif; font-size: 13.02400016784668px;" class="">
Bug fixes/deprecations:</div>
<ul style="line-height: 1.5em; padding: 0px; list-style-image:
url(https://www.openmicroscopy.org/site/bullet.gif);
list-style-type: square; margin: 0.5em 0px 0px 1.5em;
font-family: 'Lucida Grande', Verdana, Lucida, Helvetica, Arial,
sans-serif; font-size: 13.02400016784668px;" class="">
<li style="margin-bottom: 0.5em;" class="">deprecated
loci.formats.meta.MetadataConverter in favor of
ome.xml.meta.MetadataConverter</li>
<li style="margin-bottom: 0.5em;" class="">updated method
deprecated in Octave 4.2.0 (thanks to Carnë Draug)</li>
<li style="margin-bottom: 0.5em;" class="">OME-XML
<ul style="line-height: 1.5em; padding: 0px; list-style-image:
url(https://www.openmicroscopy.org/site/bullet.gif);
list-style-type: square; margin: 0.5em 0px 0px 1.5em;"
class="">
<li style="margin-bottom: 0.5em;" class="">fixed handling of
Mask BinData elements</li>
</ul>
</li>
</ul>
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font-family: 'Lucida Grande', Verdana, Lucida, Helvetica, Arial,
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Component architecture changes/decoupling:</div>
<ul style="line-height: 1.5em; padding: 0px; list-style-image:
url(https://www.openmicroscopy.org/site/bullet.gif);
list-style-type: square; margin: 0.5em 0px 0px 1.5em;
font-family: 'Lucida Grande', Verdana, Lucida, Helvetica, Arial,
sans-serif; font-size: 13.02400016784668px;" class="">
<li style="margin-bottom: 0.5em;" class="">removed
formats-common component - now decoupled to the new
ome/ome-common-java GitHub repository and consumed as
‘org.openmicroscopy:ome-common’ artifact from Maven Central</li>
<li style="margin-bottom: 0.5em;" class="">removed ome-poi
component - now decoupled to the new ome/ome-poi GitHub
repository and consumed as ‘org.openmicroscopy:ome-poi’
artifact from Maven Central</li>
<li style="margin-bottom: 0.5em;" class="">removed
specification, xsd-fu and ome-xml components - now decoupled
to the new ome/ome-model GitHub repository and consumed as
‘org.openmicroscopy:{specification,ome-xml}’ artifacts from
Maven Central</li>
<li style="margin-bottom: 0.5em;" class="">removed mdbtools
component - now decoupled to the new ome/ome-mdbtools GitHub
repository and consumed as ‘org.openmicroscopy:ome-mdbtools’
artifact from Maven Central</li>
<li style="margin-bottom: 0.5em;" class="">removed stubs
components - now decoupled to the new ome/ome-stubs GitHub
repository and consumed as
‘org.openmicroscopy:{lwf-stubs,mipav-stubs}’ artifacts from
Maven Central</li>
<li style="margin-bottom: 0.5em;" class="">removed metakit
component - now decoupled to the new ome/ome-metakit GitHub
repository and consumed as ‘org.openmicroscopy:metakit’
artifacts from Maven Central</li>
<li style="margin-bottom: 0.5em;" class="">updated developer
documentation for the decoupled components</li>
</ul>
<div style="margin: 0px 0px 0.75em; line-height: 1.5em;
font-family: 'Lucida Grande', Verdana, Lucida, Helvetica, Arial,
sans-serif; font-size: 13.02400016784668px;" class="">
Updated build system:</div>
<ul style="line-height: 1.5em; padding: 0px; list-style-image:
url(https://www.openmicroscopy.org/site/bullet.gif);
list-style-type: square; margin: 0.5em 0px 0px 1.5em;
font-family: 'Lucida Grande', Verdana, Lucida, Helvetica, Arial,
sans-serif; font-size: 13.02400016784668px;" class="">
<li style="margin-bottom: 0.5em;" class="">dropped embedded JARs
and now use the Maven Ant Tasks plugin to unify the
dependencies using the POM</li>
<li style="margin-bottom: 0.5em;" class="">improved Ant JAR and
bundle target</li>
<li style="margin-bottom: 0.5em;" class="">dropped deprecated
osgi targets, OME Tools bundle and ome-jxr component</li>
<li style="margin-bottom: 0.5em;" class="">removed PDF
generation from the docs-sphinx target</li>
<li style="margin-bottom: 0.5em;" class="">added version number
to Javadoc zip bundle name</li>
<li style="margin-bottom: 0.5em;" class="">migrated unit tests
out of test-suite into formats-bsd</li>
<li style="margin-bottom: 0.5em;" class="">fixed test-suite
targets, paths and symlink handling</li>
<li style="margin-bottom: 0.5em;" class="">fixed test-metadata
and migrated it into test-suite</li>
<li style="margin-bottom: 0.5em;" class="">fixed mismatch
between ND2HandlerTest package and location</li>
<li style="margin-bottom: 0.5em;" class="">cleaned up test-build
to remove obsolete and decoupled components and folders
simplified Travis build</li>
<li style="margin-bottom: 0.5em;" class="">POM repositories
clean-up to reduce complexity and use Maven Central as the
first location to look for dependencies</li>
<li style="margin-bottom: 0.5em;" class="">now storing all
versions in the top-level POM</li>
<li style="margin-bottom: 0.5em;" class="">updated build
versioning from Maven by unified versioning strategy,
reviewing meta information stored in the manifests of each JAR
and introspecting this information in the FormatTools API to
retrieve version and revision numbers</li>
<li style="margin-bottom: 0.5em;" class="">updated developer
documentation on updated build system</li>
</ul>
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Full details can be found at <a moz-do-not-send="true"
href="http://www.openmicroscopy.org/site/support/bio-formats5.3/about/whats-new.html"
class="">
http://www.openmicroscopy.org/site/support/bio-formats5.3/about/whats-new.html</a></div>
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sans-serif; font-size: 13.02400016784668px;" class="">
The software is available at:</div>
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sans-serif; font-size: 13.02400016784668px;" class="">
<a moz-do-not-send="true"
href="http://downloads.openmicroscopy.org/bio-formats/5.3.0"
class="">http://downloads.openmicroscopy.org/bio-formats/5.3.0</a></div>
<div style="margin: 0px 0px 0.75em; line-height: 1.5em;
font-family: 'Lucida Grande', Verdana, Lucida, Helvetica, Arial,
sans-serif; font-size: 13.02400016784668px;" class="">
and is available from the Java 8 update site for Fiji users
(note that you will need to disable the 'Bio-Formats 5' update
site if you currently have it enabled, as well as enabling the
'Java 8' updates - this functionality is available under "Manage
update sites").</div>
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font-family: 'Lucida Grande', Verdana, Lucida, Helvetica, Arial,
sans-serif; font-size: 13.02400016784668px;" class="">
Any problems or comments, please use the OME Forums or mailing
lists:</div>
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<a moz-do-not-send="true"
href="http://www.openmicroscopy.org/site/community" class="">http://www.openmicroscopy.org/site/community</a></div>
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Regards,</div>
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The OME Team</div>
<div style="margin: 0px 0px 0.75em; line-height: 1.5em;
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sans-serif; font-size: 13.02400016784668px;" class="">
<br class="">
</div>
<div class="">
<div class="">
<div class="">Dr Helen Flynn</div>
<div class="">OME Technical Writer</div>
<div class="">Centre for Gene Regulation & Expression</div>
<div class="">Open Microscopy Environment</div>
<div class="">University of Dundee</div>
<div class=""><a moz-do-not-send="true"
href="http://openmicroscopy.org/" class="">http://openmicroscopy.org</a></div>
</div>
</div>
<br class="">
<br>
<span style="font-size:10pt;">The University of Dundee is a
registered Scottish Charity, No: SC015096</span>
</blockquote>
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