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<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 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 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 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 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>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> ome-users [mailto:ome-users-bounces@lists.openmicroscopy.org.uk]
<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 <ome-users@lists.openmicroscopy.org.uk><br>
<b>Subject:</b> Re: [ome-users] Omero.tables view for images<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Frederik, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<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>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">We don’t yet support the same functionality with images in Datasets. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<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>
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<p class="MsoNormal">OMERO.tables on Datasets) so we can plan for supporting this in the future.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Cheers,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Will.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On 26 Oct 2016, at 09:00, Frederik Grüll <<a href="mailto:frederik.gruell@unibas.ch">frederik.gruell@unibas.ch</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<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 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>
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<p class="MsoNormal">On 25.10.2016 14:16, Simon Li wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Hi Frederik<o:p></o:p></p>
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<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 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>
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<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>
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<p class="MsoNormal"><o:p> </o:p></p>
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<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 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 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 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 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>
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<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>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Hope this helps<o:p></o:p></p>
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<p class="MsoNormal">Simon<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On 25 October 2016 at 10:54, Frederik Grüll <<a href="mailto:frederik.gruell@unibas.ch" target="_blank">frederik.gruell@unibas.ch</a>> wrote:<o:p></o:p></p>
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<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 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 href="tel:%2B41%20%2861%29%20207%202250">
+41 (61) 207 2250</a> |<br>
<a href="mailto:frederik.gruell@unibas.ch">frederik.gruell@unibas.ch</a> | <a 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>
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<p class="MsoNormal"><o:p> </o:p></p>
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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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<o:p></o:p></p>
<pre>_______________________________________________<o:p></o:p></pre>
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<p class="MsoNormal"><o:p> </o:p></p>
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<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 href="mailto:frederik.gruell@unibas.ch">frederik.gruell@unibas.ch</a> | <a href="http://www.biozentrum.unibas.ch/">
www.biozentrum.unibas.ch</a><o:p></o:p></p>
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<span style="font-size:10.0pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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