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Hi Frederik,
<div class=""><br class="">
</div>
<div class=""> Yes, it seems that it’s only the clients that need updating to support Images.</div>
<div class=""><br class="">
</div>
<div class="">Although we currently show Well and Image together in the right panel (image depends on which field the plate is selected for the plate)</div>
<div class="">this is changing in OMERO 5.3:</div>
<div class="">The right panel will only show the Well when it’s chosen from the Plate, the containing images will be shown below the main plate,</div>
<div class="">and clicking these images will load the Image in the right panel.</div>
<div class="">This means that you can choose whether to annotate the Well or the contained Images.</div>
<div class="">See <a href="https://github.com/openmicroscopy/openmicroscopy/pull/4863" class="">https://github.com/openmicroscopy/openmicroscopy/pull/4863</a> (feedback welcome)!</div>
<div class=""><br class="">
</div>
<div class="">I’ll make sure we update the display of Tables data, so that when you choose an Image you see any Tables data on Images.</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class=""><br class="">
</div>
<div class=""> Will.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 31 Oct 2016, at 12:45, Frederik Grüll <<a href="mailto:frederik.gruell@unibas.ch" class="">frederik.gruell@unibas.ch</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
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<p class="">Hi Will, all,</p>
<p class="">Thank you for the clarification. I did a few tests with the Populate Metadata script and it picked up the column with the image ID as expected and wrote it into the HDF file (bulk_annotations) with the right column type (::omero::grid::ImageColumn).
It even added the image name as an extra column. So I think only the presentation in the clients would need to be updated. I have attached the CSV file I used for testing and the resulting HDF for reference.<br class="">
</p>
<p class="">The feature would be nice to have. In the meantime I'm good because I think I can work with the Key-Value Pairs as a replacement.<br class="">
</p>
<p class="">Cheers and thanks again,</p>
<p class="">Frederik<br class="">
</p>
<br class="">
<div class="moz-cite-prefix">On 31.10.2016 13:24, William Moore (Staff) wrote:<br class="">
</div>
<blockquote cite="mid:369E61E5-FBE2-4FA9-B82E-DA235952B98E@dundee.ac.uk" type="cite" class="">
Hi Frederik,
<div class=""><br class="">
</div>
<div class=""> Ah, OK - sorry I misunderstood you there.</div>
<div class="">Yes, I’m afraid that we only support the display of OMERO.tables data associated with Wells, not Images within the Well.</div>
<div class=""><br class="">
</div>
<div class="">But, again, if this feature is important for you, let us know so we can consider adding it.</div>
<div class="">I’ve added this to the card at <a moz-do-not-send="true" href="https://trello.com/c/iFe4XS0z/51-refactor-rewrite-populate-metadata-py" class="">https://trello.com/c/iFe4XS0z/51-refactor-rewrite-populate-metadata-py</a>.</div>
<div class=""><br class="">
</div>
<div class=""> Cheers,</div>
<div class=""><br class="">
</div>
<div class=""> Will.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 28 Oct 2016, at 09:20, Frederik Grüll <<a moz-do-not-send="true" href="mailto:frederik.gruell@unibas.ch" class="">frederik.gruell@unibas.ch</a>> wrote:</div>
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<div class="">
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<p class="">Hi Will, all,</p>
<p class="">The key-value annotations work well so far. I have one line per image in an attached CSV file and I can easily parse this data and annotate it with an OMERO script as a key-value map. The CSV file is created by CellProfiler and I just loop the image
IDs through it with the LoadData module.</p>
<p class="">My image data is actually organized in plates, but I could not make an OMERO table that would show metadata per image instead of metadata per well, even if I substitute the well column with an image column in the HDF file that backs the table.<br class="">
</p>
<p class="">Cheers,</p>
<p class="">Frederik<br class="">
</p>
<br class="">
<div class="moz-cite-prefix">On 27.10.2016 17:11, William Moore (Staff) wrote:<br class="">
</div>
<blockquote cite="mid:288C425E-23E0-48CE-97D9-F8154BEF12E1@dundee.ac.uk" type="cite" class="">
Hi Frederik,
<div class=""><br class="">
</div>
<div class=""> The Glencoe webinar is only using HCS data (all the images are in Wells & Plates) with the tables data attached to the Plate/Screen.</div>
<div class=""><br class="">
</div>
<div class="">We don’t yet support the same functionality with images in Datasets. </div>
<div class=""><br class="">
</div>
<div class="">Let us know if you have any issues with using Key-Value “Map” annotations (and if you need</div>
<div class="">OMERO.tables on Datasets) so we can plan for supporting this in the future.</div>
<div class=""><br class="">
</div>
<div class=""> Cheers,</div>
<div class=""><br class="">
</div>
<div class=""> Will.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 26 Oct 2016, at 09:00, Frederik Grüll <<a moz-do-not-send="true" href="mailto:frederik.gruell@unibas.ch" class="">frederik.gruell@unibas.ch</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
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<p class="">Hi Simon,</p>
<p class="">Thank you for your answer. I think I will go with the key-value store.<br class="">
</p>
<p class="">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 class="">
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="https://glencoesoftware.com/webinars.html">https://glencoesoftware.com/webinars.html</a><br class="">
</p>
<p class="">Cheers,</p>
<p class="">Frederik<br class="">
</p>
<br class="">
<div class="moz-cite-prefix">On 25.10.2016 14:16, Simon Li wrote:<br class="">
</div>
<blockquote cite="mid:CAMvbRBGaDXa6XfUpBnodL_acUE+007sNa7xwZiuap_bS6T7Xrg@mail.gmail.com" type="cite" class="">
<div dir="ltr" class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div class="">Hi Frederik<br class="">
<br class="">
</div>
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" class="">
http://idr-demo.openmicroscopy<wbr class="">.org/webclient/?show=image-192<wbr class="">0093</a><br class="">
<br class="">
</div>
<div class="">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.<br class="">
</div>
<br class="">
</div>
It's still considered "developmental", but you can see previousl conversations on the topic here:<br class="">
- <a moz-do-not-send="true" href="http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2016-June/003694.html" target="_blank" class="">
http://lists.openmicroscopy.or<wbr class="">g.uk/pipermail/ome-devel/2016-<wbr class="">June/003694.html</a><br class="">
- <a moz-do-not-send="true" href="http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2016-August/003733.html" target="_blank" class="">
http://lists.openmicroscopy.<wbr class="">org.uk/pipermail/ome-devel/<wbr class="">2016-August/003733.html</a><br class="">
<br class="">
And some example configuration files here:<br class="">
<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" class="">- https://github.com/IDR/idr-met<wbr class="">adata/blob/master/idr0018-neff<wbr class="">-histopathology/experimentA/<wbr class="">idr0018-experimentA-<wbr class="">annotation.csv</a><br class="">
<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" class="">- https://github.com/IDR/idr-met<wbr class="">adata/blob/master/idr0018-neff<wbr class="">-histopathology/experimentA/<wbr class="">idr0018-experimentA-bulkmap-<wbr class="">config.yml</a><br class="">
<br class="">
</div>
I'll have to check whether the support for populating Images in Datasets made it into the last release.<br class="">
<br class="">
</div>
<div class="">Hope this helps<br class="">
<br class="">
</div>
Simon<br class="">
<div class="">
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<div class=""><br class="">
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<div class="gmail_extra"><br class="">
<div class="gmail_quote">On 25 October 2016 at 10:54, Frederik Grüll <span dir="ltr" class="">
<<a moz-do-not-send="true" href="mailto:frederik.gruell@unibas.ch" target="_blank" class="">frederik.gruell@unibas.ch</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">
Dear all,<br class="">
<br class="">
the OMERO webclient offers a nice overview of table data for wells in a<br class="">
screen with OMERO.tables. I can import the data with the script<br class="">
"Populate Metadata" and see it in the table accordion on the right pane.<br class="">
<br class="">
Is there a way to have the same for images instead wells? I made some<br class="">
experiments, eg. with<br class="">
<a moz-do-not-send="true" href="https://github.com/openmicroscopy/openmicroscopy/blob/v5.2.6/examples/OmeroTables/MeasurementTable.java" rel="noreferrer" target="_blank" class="">https://github.com/<wbr class="">openmicroscopy/openmicroscopy/<wbr class="">blob/v5.2.6/examples/<wbr class="">OmeroTables/MeasurementTable.<wbr class="">java</a><br class="">
and by adjusting "Populate Metadata", but could not make the table<br class="">
appear for images.<br class="">
<br class="">
Cheers,<br class="">
<br class="">
Frederik<br class="">
<br class="">
<br class="">
--<br class="">
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