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Hi Sebastien,<br>
<br>
Thank you for confirming the status of MRC and Spider changes.
Currently we do not have the specifics of DM4 format, but we are
looking into a way to provide you with such.<br>
<br>
Best regards,<br>
Andrii<br>
<br>
<div class="moz-cite-prefix">On 31/01/2017 15:00, Sebastien Besson
(Staff) wrote:<br>
</div>
<blockquote
cite="mid:75414EE6-F29B-467B-9EDF-E79A1F4C6E21@dundee.ac.uk"
type="cite">
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<div style="line-height: 1.38; margin-top: 0pt; margin-bottom:
0pt;" 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;" class="">Hi Andrii,</span></div>
<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;" class="">Answering the
Bio-Formats specifics:</span></div>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom:
0pt;" class=""><span style="font-size: 11pt; line-height:
1.38; font-family: Arial;" class="">- for MRC and Spider, as
you rightfully said, these changes are already distributed
in Bio-Formats 5.2.0 and later. This release also included
breaking model changes and is not distributed in the current
OMERO 5.2 line but these improvements will be available in
OMERO 5.3.0</span></div>
<div style="line-height: 1.38; margin-top: 0pt; margin-bottom:
0pt;" class=""><span style="font-size: 11pt; line-height:
1.38; font-family: Arial;" class="">- </span><span
style="font-size: 11pt; line-height: 1.38; font-family:
Arial;" class="">for the DM4 format, one of the major issues
is that we have no specification for this format. In order
to support new modalities, we need to collect more data
samples and assess the amount of work required to update
Bio-Formats. If you or anyone else in the community with
expertise in this modality want to be involved in the
development, please let us know.</span></div>
<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;" class="">Best,</span></div>
<span style="font-size: 11pt; font-family: Arial;
vertical-align: baseline;" class="">Sebastien</span></div>
<div class=""><font class="" face="Arial"><span style="font-size:
15px;" class=""><br class="">
</span></font>
<div>
<blockquote type="cite" class="">
<div class="">On 31 Jan 2017, at 13:19, Andrii Iudin <<a
moz-do-not-send="true" href="mailto:andrii@ebi.ac.uk"
class="">andrii@ebi.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div bgcolor="#FFFFFF" text="#000000" class="">Hi Will,<br
class="">
<br class="">
Thanks for implementing the reversion into the OMERO,
more reasons for us now to look forward to the 5.3.0
release!<br class="">
<br class="">
Best regards,<br class="">
Andrii<br class="">
<br class="">
<div class="moz-cite-prefix">On 30/01/2017 16:06,
William Moore (Staff) wrote:<br class="">
</div>
<blockquote
cite="mid:5E36148A-2DC3-4C9D-B866-3B6C02DEDD30@dundee.ac.uk"
type="cite" class="">
Hi Andrii,
<div class=""><br class="">
</div>
<div class="">In 5.3.0, “reverse intensity” will be
supported by the OMERO rendering engine and</div>
<div class="">by the clients: See web client PR <a
moz-do-not-send="true"
href="https://github.com/openmicroscopy/openmicroscopy/pull/4839"
class="">https://github.com/openmicroscopy/openmicroscopy/pull/4839</a></div>
<div class=""><br class="">
</div>
<div class="">The “reverse intensity” can be specified
per-channel, and we also support a look-up-table
per-channel.</div>
<div class=""><br class="">
</div>
<div class=""> I’ll leave the detail of Bio-Formats
tickets to a Bio-Formats dev, but can tell you that
Bio-Formats 5.2.0 will be in OMERO 5.3.0 in March.</div>
<div class=""><br class="">
</div>
<div class=""> Regards,</div>
<div class=""><br class="">
</div>
<div class=""> Will.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 30 Jan 2017, at 10:05, Andrii
Iudin <<a moz-do-not-send="true"
href="mailto:andrii@ebi.ac.uk" class="">andrii@ebi.ac.uk</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Dear OMERO Developers,<br class="">
<br class="">
With the release of 5.3.0 update approaching,
I was wondering if you might, please, tell
what is the status of the following
features/fixes?<br class="">
- Color inversion API. Initially discussed
with William Moore on 14-01-2016 in ome-devel:<br
class="">
<a moz-do-not-send="true"
href="http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2016-January/003566.html"
class="">http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2016-January/003566.html</a><br
class="">
<br class="">
We have been provided with a script to test,
approved it and it has added to the
requirements gathering for further rendering
support. However, as far as I know it is not
yet available?<br class="">
<br class="">
<br class="">
- Support of EMPIAR files. There are three
tickets for Bio-Formats:<br class="">
<a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="https://trac.openmicroscopy.org/ome/ticket/13057">https://trac.openmicroscopy.org/ome/ticket/13057</a>
(Reg: dm4 files)<br class="">
<a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="https://trac.openmicroscopy.org/ome/ticket/13058">https://trac.openmicroscopy.org/ome/ticket/13058</a>
(Reg: mrcs files)<br class="">
<a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="https://trac.openmicroscopy.org/ome/ticket/13059">https://trac.openmicroscopy.org/ome/ticket/13059</a>
(Reg: Spider files)<br class="">
<br class="">
MRCS and Spider should be implemented in
Bio-Formats 5.2.0. Which is currently not yet
supported by OMERO (would be in the March
release?).<br class="">
But DM4 has been moved to an enhancement
request list. Is this still planned to be
implemented?<br class="">
<br class="">
Many thanks and best regards,<br class="">
Andrii<br class="">
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</blockquote>
</div>
<br class="">
</div>
<br class="">
<span style="font-size:10pt;" class="">The University
of Dundee is a registered Scottish Charity, No:
SC015096</span>
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