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<p>Hi Will, all,</p>
<p>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>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>
</p>
<p>Cheers,</p>
<p>Frederik<br>
</p>
<br>
<div class="moz-cite-prefix">On 27.10.2016 17:11, William Moore
(Staff) wrote:<br>
</div>
<blockquote
cite="mid:288C425E-23E0-48CE-97D9-F8154BEF12E1@dundee.ac.uk"
type="cite">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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>
<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="">
<div bgcolor="#FFFFFF" text="#000000" class="">
<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="">
<div class=""><br class="">
<div class=""><br class="">
<br class="">
<br class="">
<div class="">
<div class=""><br class="">
</div>
</div>
</div>
</div>
</div>
</div>
<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="">
Dr. Frederik Grüll | Imaging Expert | G1055,
Biozentrum, University of<br class="">
Basel | Klingelbergstr. 50/70 | CH-4056 Basel
Phone: <a moz-do-not-send="true"
href="tel:%2B41%20%2861%29%20207%202250"
value="+41612072250" class="">
+41 (61) 207 2250</a> |<br class="">
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href="mailto:frederik.gruell@unibas.ch"
class="">frederik.gruell@unibas.ch</a> |
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<br class="">
<div class="moz-signature">-- <br class="">
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"
class="moz-txt-link-abbreviated"
href="mailto:frederik.gruell@unibas.ch">frederik.gruell@unibas.ch</a>
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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> |
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