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<p>Hi Will, all,</p>
<p>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>
</p>
<p>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>
</p>
<p>Cheers and thanks again,</p>
<p>Frederik<br>
</p>
<br>
<div class="moz-cite-prefix">On 31.10.2016 13:24, William Moore
(Staff) wrote:<br>
</div>
<blockquote
cite="mid:369E61E5-FBE2-4FA9-B82E-DA235952B98E@dundee.ac.uk"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
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>
<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>
<br class="Apple-interchange-newline">
<div class="">
<div bgcolor="#FFFFFF" text="#000000" class="">
<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="">
<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="">
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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 |
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Biozentrum, University of Basel | Klingelbergstr.
50/70 | CH-4056 Basel Phone: +41 (61) 207 2250 |
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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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