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Hi
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<div class="">What do you mean by merged images? Did you have a chance to check HCS structures (Screen, Plate and Well) of the OME Model in <a href="http://www.openmicroscopy.org/site/support/ome-model/developers/model-overview.html?" class="">http://www.openmicroscopy.org/site/support/ome-model/developers/model-overview.html?</a></div>
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<div class="">If you query DB directly to see how that is structured you could try something like</div>
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<div class="">SQL:</div>
<div class="">select w.id as well_id, ws.well_index as field, i.id as image_id</div>
<div class="">from image as i</div>
<div class=""> join wellsample as ws on (ws.image=i.id) </div>
<div class=""> join well as w on (ws.well=w.id)</div>
<div class=""> join plate as p on (w.plate=p.id)</div>
<div class=""> join screenplatelink as spl on (spl.child=p.id)</div>
<div class="">where spl.parent = :screen_id</div>
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<div class="">Using omero api you could try HQL query and filter by tag value:</div>
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<div style="margin: 0px; line-height: normal;" class="">ParametersI <span style="color: #7e504f" class="">
param</span> = <span style="color: #931a68" class="">new</span> ParametersI();</div>
<div style="margin: 0px; line-height: normal;" class=""><span style="color: #7e504f" class="">param</span>.<span style="color: #0326cc" class="">map</span>.put(<span style="color: #3933ff" class="">"sid"</span>, omero.rtypes.rlong(102));</div>
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<div style="margin: 0px; line-height: normal;" class="">StringBuffer <span style="color: #7e504f" class="">
sb</span> = <span style="color: #931a68" class="">new</span> StringBuffer();</div>
<div style="margin: 0px; line-height: normal; color: rgb(57, 51, 255);" class="">
<span style="color: #7e504f" class="">sb</span><span style="color: #000000" class="">.append(</span>"select new map( w.id as wellid, index(ws) as field, i.id as imgid) "<span style="color: #000000" class="">); </span></div>
<div style="margin: 0px; line-height: normal; color: rgb(57, 51, 255);" class="">
<span style="color: #7e504f" class="">sb</span><span style="color: #000000" class="">.append(</span>"from Well w "<span style="color: #000000" class="">); </span></div>
<div style="margin: 0px; line-height: normal; color: rgb(57, 51, 255);" class="">
<span style="color: #7e504f" class="">sb</span><span style="color: #000000" class="">.append(</span>"join w.wellSamples ws "<span style="color: #000000" class="">); </span></div>
<div style="margin: 0px; line-height: normal; color: rgb(57, 51, 255);" class="">
<span style="color: #7e504f" class="">sb</span><span style="color: #000000" class="">.append(</span>"join ws.image i "<span style="color: #000000" class="">);</span></div>
<div style="margin: 0px; line-height: normal; color: rgb(57, 51, 255);" class="">
<span style="color: #7e504f" class="">sb</span><span style="color: #000000" class="">.append(</span>"join i.annotationLinks ial "<span style="color: #000000" class="">);</span></div>
<div style="margin: 0px; line-height: normal; color: rgb(57, 51, 255);" class="">
<div style="margin: 0px; line-height: normal;" class=""><span style="color: #7e504f" class="">sb</span><span style="color: #000000" class="">.append(</span>"join ial.child tag "<span style="color: #000000" class="">);</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="color: #7e504f" class="">sb</span><span style="color: #000000" class="">.append(</span>"join w.plate pl "<span style="color: #000000" class="">); </span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="color: #7e504f" class="">sb</span><span style="color: #000000" class="">.append(</span>"join pl.screenLinks sl "<span style="color: #000000" class="">); </span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="color: #7e504f" class="">sb</span><span style="color: #000000" class="">.append(</span>"join sl.parent s "<span style="color: #000000" class="">); </span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="color: #7e504f" class="">sb</span><span style="color: #000000" class="">.append(</span>"where s.id = :sid “<span style="color: rgb(0, 0, 0);" class="">);</span></div>
<div style="margin: 0px; line-height: normal;" class=""><span style="color: rgb(126, 80, 79);" class="">sb</span><span style="color: rgb(0, 0, 0);" class="">.append(</span>"and tag.class = TagAnnotation and tag.textValue = 'error' “<span style="color: #000000" class="">);</span></div>
<div style="margin: 0px; line-height: normal;" class=""><br class="">
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<div style="margin: 0px; line-height: normal;" class=""><span style="color: #931a68" class="">for</span> (<span style="color: #931a68" class="">final</span> List<RType>
<span style="color: #7e504f" class="">result</span> : <span style="color: #7e504f" class="">
queryService</span>.projection(<span style="color: #7e504f" class="">sb</span>.toString(),
<span style="color: #7e504f" class="">param</span>)) {</div>
<div style="margin: 0px; line-height: normal;" class=""> System.<span style="color: #0326cc" class="">out</span>.println(omero.rtypes.unwrap(<span style="color: #7e504f" class="">result</span>.get(0)));</div>
<div style="margin: 0px; line-height: normal;" class="">}</div>
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<div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Monaco;" class="">
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<div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Monaco;" class="">
depends on which version of OMERO.jar you are using annotation discriminator may be <span style="text-decoration: underline;" class="">/basic</span>/<span style="text-decoration: underline;" class="">text</span>/<span style="text-decoration: underline;" class="">tag</span>/
(this was fixed in 5.3-develop to map the class <span style="color: rgb(57, 51, 255);" class="">TagAnnotation)</span></div>
<div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Monaco;" class="">
<div style="margin: 0px; line-height: normal;" class=""><br class="">
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<div class="">Hope that helps</div>
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Kind regards</div>
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Ola</div>
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Software Engineer</div>
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Open Microscopy Environment</div>
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University of Dundee</div>
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<blockquote type="cite" class="">
<div class="">On 9 Feb 2017, at 15:36, Jäälinoja, Harri Tapio <<a href="mailto:harri.jaalinoja@helsinki.fi" class="">harri.jaalinoja@helsinki.fi</a>> wrote:</div>
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<div class="">Hi,<br class="">
<br class="">
this is continuation of my previous question about browsing a plate with the Java API. I've uploaded a couple of plates, in the database it looks like this:<br class="">
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select id,name from image order by id;<br class="">
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id | name <br class="">
------+-----------------------------------------------------------------<br class="">
1 | LMU-CELLINSIGHT_170111150001_B03f00d0.C01 [Well B03, Field #00]<br class="">
...<br class="">
1920 | LMU-CELLINSIGHT_150428120001_B05f00d0.C01 [Well B05, Field #15]<br class="">
(1920 rows)<br class="">
<br class="">
So the database only has the merged images of each field in well. The original files are on the OMERO server, but it seems it's not possible to find them with a URL like "omero::iid=123"?<br class="">
<br class="">
What I have in mind is to pick a plateID and build a corresponding CSV formatted image list for CellProfiler LoadData module (see
<a href="https://github.com/CellProfiler/CellProfiler/wiki/OMERO:-Accessing-images-from-CellProfiler" class="">
https://github.com/CellProfiler/CellProfiler/wiki/OMERO:-Accessing-images-from-CellProfiler</a>). Something like:<br class="">
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URL_DAPI,URL_GFP,URL_CY5<br class="">
omero::iid=123,omero::iid=124,omero::iid=125<br class="">
<br class="">
(Ideally the image list would exclude fields tagged by the user as imaging errors.)<br class="">
Is this possible at the moment? If not, would it a reasonable request?<br class="">
<br class="">
Best,<br class="">
Harri<br class="">
<br class="">
---<br class="">
Harri Jäälinoja<br class="">
Light Microscopy Unit<br class="">
Institute of Biotechnology<br class="">
University of Helsinki<br class="">
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</blockquote>
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