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<p>Hi Steve,</p>
<p>Thank you for the link. At the moment we are going for automated
image analysis for one or two plates only and not high-content
screens. I will keep it in mind, the visualization looks
definitely impressive.<br>
</p>
<p>Kind regards,<br>
</p>
<p>Frederik<br>
</p>
<br>
<div class="moz-cite-prefix">On 27.10.2016 22:48, Stephen Taylor
wrote:<br>
</div>
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<div class="WordSection1">
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi
Frederik,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Have
you seen Zegami? This is a useful way to visualise HCS data
since it allows querying of the tables after caching OMERO
data and also allows linking direct to OMERO. Here is a link
to a demo:<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><a
moz-do-not-send="true"
href="http://demo.zegami.com/omero-idr.html">http://demo.zegami.com/omero-idr.html</a><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Briefly,
facets on the left of the Zegami GUI allow rapid querying of
the metadata and this is reflected in the zoomable interface
which shows images of the wells. If you click on a well this
brings up a metadata panel which shows the data relating to
the image. At the top of the panel is an icon of a flask
linked to the OMERO Insight Viewer which will give direct
access to the raw images stored in OMERO.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">More
info about Zegami here:<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><a
moz-do-not-send="true" href="https://www.zegami.com/">https://www.zegami.com/</a><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Just
to be clear, Zegami is spin-out company from Oxford
University, and I am one of the founders. There are free for
academic versions as well as paid for versions. I’d be
interested to know if it’s useful for your needs. <o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Kind
regards and thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Steve<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">=======================================<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Head
of Computational Biology Research Group
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Weatherall
Institute of Molecular Medicine
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">University
of Oxford
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">+44
1865 222640<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><a
moz-do-not-send="true" href="http://www.cbrg.ox.ac.uk/"><span
style="color:#0563C1">www.cbrg.ox.ac.uk</span></a>
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><a moz-do-not-send="true"
name="_MailEndCompose"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></a></p>
<div style="border:none;border-left:solid blue 1.5pt;padding:0cm
0cm 0cm 4.0pt">
<div>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif"
lang="EN-US">From:</span></b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif"
lang="EN-US"> ome-users
[<a class="moz-txt-link-freetext" href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</a>]
<b>On Behalf Of </b>William Moore (Staff)<br>
<b>Sent:</b> 27 October 2016 16:12<br>
<b>To:</b> OME User Support List
<a class="moz-txt-link-rfc2396E" href="mailto:ome-users@lists.openmicroscopy.org.uk"><ome-users@lists.openmicroscopy.org.uk></a><br>
<b>Subject:</b> Re: [ome-users] Omero.tables view for
images<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Frederik, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"> The Glencoe webinar is only using HCS
data (all the images are in Wells & Plates) with the
tables data attached to the Plate/Screen.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">We don’t yet support the same
functionality with images in Datasets. <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Let us know if you have any issues with
using Key-Value “Map” annotations (and if you need<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">OMERO.tables on Datasets) so we can
plan for supporting this in the future.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"> Cheers,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"> Will.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On 26 Oct 2016, at 09:00,
Frederik Grüll <<a moz-do-not-send="true"
href="mailto:frederik.gruell@unibas.ch">frederik.gruell@unibas.ch</a>>
wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi
Simon,<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thank
you for your answer. I think I will go with the
key-value store.<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I
saw table information for images in the webinar
"OMERO Plus for High Content Screening &
Analysis" at 0:46:04. Is this only supported by
OMERO Plus?<br>
<a moz-do-not-send="true"
href="https://glencoesoftware.com/webinars.html">https://glencoesoftware.com/webinars.html</a><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Cheers,<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Frederik<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On 25.10.2016 14:16, Simon Li
wrote:<o:p></o:p></p>
</div>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"
style="margin-bottom:12.0pt">Hi
Frederik<o:p></o:p></p>
</div>
<p class="MsoNormal"
style="margin-bottom:12.0pt">We don't
have a way of directly displaying
Table information alongside images at
the moment. However we've done some
related work for the IDR project,
where we built a CLI plugin to convert
a table into MapAnnotations on images,
e.g. see the Key-Value pairs on <a
moz-do-not-send="true"
href="http://idr-demo.openmicroscopy.org/webclient/?show=image-1920093"
target="_blank">
http://idr-demo.openmicroscopy.org/webclient/?show=image-1920093</a><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">The main rationale
for this approach was to distinguish
between the raw data held in the
table, and the client-visible view of
that data.<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal"
style="margin-bottom:12.0pt">It's still
considered "developmental", but you can
see previousl conversations on the topic
here:<br>
- <a moz-do-not-send="true"
href="http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2016-June/003694.html"
target="_blank">
http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2016-June/003694.html</a><br>
- <a moz-do-not-send="true"
href="http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2016-August/003733.html"
target="_blank">
http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2016-August/003733.html</a><br>
<br>
And some example configuration files here:<br>
<a moz-do-not-send="true"
href="https://github.com/IDR/idr-metadata/blob/master/idr0018-neff-histopathology/experimentA/idr0018-experimentA-annotation.csv"
target="_blank">-
https://github.com/IDR/idr-metadata/blob/master/idr0018-neff-histopathology/experimentA/idr0018-experimentA-annotation.csv</a><br>
<a moz-do-not-send="true"
href="https://github.com/IDR/idr-metadata/blob/master/idr0018-neff-histopathology/experimentA/idr0018-experimentA-bulkmap-config.yml"
target="_blank">-
https://github.com/IDR/idr-metadata/blob/master/idr0018-neff-histopathology/experimentA/idr0018-experimentA-bulkmap-config.yml</a><o:p></o:p></p>
</div>
<p class="MsoNormal"
style="margin-bottom:12.0pt">I'll have to
check whether the support for populating
Images in Datasets made it into the last
release.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-bottom:12.0pt">Hope this helps<o:p></o:p></p>
</div>
<p class="MsoNormal">Simon<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal"
style="margin-bottom:12.0pt"><br>
<br>
<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On 25 October 2016 at
10:54, Frederik Grüll <<a
moz-do-not-send="true"
href="mailto:frederik.gruell@unibas.ch"
target="_blank">frederik.gruell@unibas.ch</a>>
wrote:<o:p></o:p></p>
<blockquote
style="border:none;border-left:solid #CCCCCC
1.0pt;padding:0cm 0cm 0cm
6.0pt;margin-left:4.8pt;margin-right:0cm">
<p class="MsoNormal"
style="margin-bottom:12.0pt">Dear all,<br>
<br>
the OMERO webclient offers a nice overview
of table data for wells in a<br>
screen with OMERO.tables. I can import the
data with the script<br>
"Populate Metadata" and see it in the
table accordion on the right pane.<br>
<br>
Is there a way to have the same for images
instead wells? I made some<br>
experiments, eg. with<br>
<a moz-do-not-send="true"
href="https://github.com/openmicroscopy/openmicroscopy/blob/v5.2.6/examples/OmeroTables/MeasurementTable.java"
target="_blank">https://github.com/openmicroscopy/openmicroscopy/blob/v5.2.6/examples/OmeroTables/MeasurementTable.java</a><br>
and by adjusting "Populate Metadata", but
could not make the table<br>
appear for images.<br>
<br>
Cheers,<br>
<br>
Frederik<br>
<br>
<br>
--<br>
Dr. Frederik Grüll | Imaging Expert |
G1055, Biozentrum, University of<br>
Basel | Klingelbergstr. 50/70 | CH-4056
Basel Phone: <a moz-do-not-send="true"
href="tel:%2B41%20%2861%29%20207%202250">
+41 (61) 207 2250</a> |<br>
<a moz-do-not-send="true"
href="mailto:frederik.gruell@unibas.ch">frederik.gruell@unibas.ch</a>
| <a moz-do-not-send="true"
href="http://www.biozentrum.unibas.ch/"
target="_blank">
www.biozentrum.unibas.ch</a><br>
<br>
<br>
The University of Dundee is a registered
Scottish Charity, No: SC015096<br>
<br>
_______________________________________________<br>
ome-users mailing list<br>
<a moz-do-not-send="true"
href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
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href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users"
target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><o:p></o:p></p>
</blockquote>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal"><br>
<span style="font-size:10.0pt">The University of
Dundee is a registered Scottish Charity, No:
SC015096</span>
<br>
<br>
<br>
<o:p></o:p></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>ome-users mailing list<o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">-- <br>
Dr. Frederik Grüll | Imaging Expert | G1055,
Biozentrum, University of Basel |
Klingelbergstr. 50/70 | CH-4056 Basel Phone: +41
(61) 207 2250 |
<a moz-do-not-send="true"
href="mailto:frederik.gruell@unibas.ch">frederik.gruell@unibas.ch</a>
| <a moz-do-not-send="true"
href="http://www.biozentrum.unibas.ch/">
www.biozentrum.unibas.ch</a><o:p></o:p></p>
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<p class="MsoNormal">_______________________________________________<br>
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<p class="MsoNormal"><br>
<span style="font-size:10.0pt">The University of Dundee is a
registered Scottish Charity, No: SC015096</span>
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<pre wrap="">_______________________________________________
ome-users mailing list
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<br>
<div class="moz-signature">-- <br>
Dr. Frederik Grüll | Imaging Expert | G1055, Biozentrum,
University of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
Phone: +41 (61) 207 2250 | <a class="moz-txt-link-abbreviated" href="mailto:frederik.gruell@unibas.ch">frederik.gruell@unibas.ch</a> |
<a class="moz-txt-link-abbreviated" href="http://www.biozentrum.unibas.ch">www.biozentrum.unibas.ch</a></div>
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