<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Harri,<div class=""><br class=""></div><div class=""> See the script service example at </div><div class=""><a href="https://github.com/openmicroscopy/openmicroscopy/blob/develop/examples/Training/python/Scripting_Service_Example.py" class="">https://github.com/openmicroscopy/openmicroscopy/blob/develop/examples/Training/python/Scripting_Service_Example.py</a></div><div class=""><br class=""></div><div class="">You just need to replace “Image” and imageId with “Plate” & plateId etc everywhere.</div><div class="">Then put the plate processing code in the place indicated.</div><div class=""><br class=""></div><div class="">(NB: this only handles a single object (plate/image) at at time. Add an extra for loop if you want to handle multiple plates).</div><div class=""><br class=""></div><div class="">You can probably remove all the conn.SERVICE_OPTS (group context) lines</div><div class="">if you’re using the script service, since it should set the context correctly anyway.</div><div class=""><br class=""></div><div class="">Then you can upload it as described</div><div class=""><a href="http://www.openmicroscopy.org/site/support/omero5.2/developers/scripts/user-guide.html#upload-script" class="">http://www.openmicroscopy.org/site/support/omero5.2/developers/scripts/user-guide.html#upload-script</a></div><div class=""><br class=""></div><div class=""> Hope that helps,</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 12 May 2016, at 17:42, Jäälinoja, Harri Tapio <<a href="mailto:harri.jaalinoja@helsinki.fi" class="">harri.jaalinoja@helsinki.fi</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi Will,</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">cool, thanks! I ran it from command line on the server as omero user, as that's where I have the omero modules. Would it be possible to install the same on the server so that you can run it from the script menu? Maybe that should be left as an exercise for me :) </div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I'm waiting for a new server where to set this up, with the specific aim of helping our CellInsight users. Of course some of them may still want to image the whole plate, so this fix wouldn't be enough, but some might agree to leave an empty column just to get the benefit of browsing the data easier.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Best,</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Harri</div></div><hr tabindex="-1" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; display: inline-block; width: 788.890625px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class=""></span><div id="divRplyFwdMsg" dir="ltr" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a>> on behalf of William Moore <<a href="mailto:will@lifesci.dundee.ac.uk" class="">will@lifesci.dundee.ac.uk</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>12 May 2016 17:32:33<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>OME User Support List<br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ome-users] Cellomics plate view column index off</font><div class=""> </div></div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">Hi Harri,<div class=""><br class=""></div><div class=""> I played a bit with a Python script to fix the Well offset,</div><div class="">but unfortunately the 12th column is still missing (not imported at-all).</div><div class="">But maybe useful if the 12th column is not used for a Plate?</div><div class=""><br class=""></div><div class=""> Will.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div class="">from omero.rtypes import rint</div><div class="">from omero.gateway import BlitzGateway</div><div class="">conn = BlitzGateway(USERNAME, PASSWORD, host="localhost", port=4064)</div><div class="">conn.connect()</div><div class=""><br class=""></div><div class="">conn.SERVICE_OPTS.setOmeroGroup("-1")</div><div class="">plate = conn.getObject("Plate", 4468)</div><div class="">gid = plate.getDetails().group.id.val</div><div class="">conn.SERVICE_OPTS.setOmeroGroup(gid)</div><div class=""><br class=""></div><div class="">wellGrid = plate.getWellGrid()</div><div class=""><br class=""></div><div class="">for row in wellGrid:</div><div class=""> toSave = []</div><div class=""> for w in row:</div><div class=""> if w is not None:</div><div class=""> well = w._obj</div><div class=""> col = well.column.val</div><div class=""> print col</div><div class=""> well.column = rint(col - 1)</div><div class=""> toSave.append(well)</div><div class=""> conn.getUpdateService().saveArray(toSave)</div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div class=""><blockquote type="cite" class=""><div class="">On 12 May 2016, at 13:58, Jäälinoja, Harri Tapio <<a href="mailto:harri.jaalinoja@helsinki.fi" class="">harri.jaalinoja@helsinki.fi</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" class="" style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;"><div class="" style="margin-top: 0px; margin-bottom: 0px;">Hi Will,</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">it's the same in Insight client:</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><a href="https://wiki.helsinki.fi/display/LMU/OMERO+troubleshooting?preview=/196947403/196949286/omeroi_cellomics.png" id="LPlnk126472" title="https://wiki.helsinki.fi/display/LMU/OMERO+troubleshooting?preview=/196947403/196949286/omeroi_cellomics.png
Ctrl+Click or tap to follow the link" class="">https://wiki.helsinki.fi/display/LMU/OMERO+troubleshooting?preview=/196947403/196949286/omeroi_cellomics.png</a></div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">I uploaded a full plate, one field per well, about 20MB.</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">Thanks!</div><div class="" style="margin-top: 0px; margin-bottom: 0px;">Harri<br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><img class="" src="https://wiki.helsinki.fi/display/LMU/OMERO+troubleshooting?preview=/196947403/196949286/omeroi_cellomics.png"></div><p class="" style="margin-top: 0px; margin-bottom: 0px;"></p></div><hr tabindex="-1" class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; display: inline-block; width: 792.8125px;"><span class="Apple-converted-space"> </span><span class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;"></span><span class="Apple-converted-space"> </span><div id="divRplyFwdMsg" dir="ltr" class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><font face="Calibri, sans-serif" class="" style="font-size: 11pt;"><b class="">From:</b><span class="Apple-converted-space"> </span>ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a>> on behalf of William Moore <<a href="mailto:will@lifesci.dundee.ac.uk" class="">will@lifesci.dundee.ac.uk</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>12 May 2016 12:57:37<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>OME User Support List<br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ome-users] Cellomics plate view column index off</font><div class=""> </div></div><div class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">Hi Harri,<div class=""><br class=""></div><div class="">I wonder if you could check whether you get the same UI issue in the Insight client?</div><div class="">If so, then this is likely an issue with initial reading of the Plate on import.</div><div class="">The easiest way for us to look at this would be if you could send us an example file.</div><div class="">Do you have an example that is quite small?</div><div class="">If you could upload it at <a href="https://www.openmicroscopy.org/qa2/qa/upload/" class="">https://www.openmicroscopy.org/qa2/qa/upload/</a></div><div class="">that would be great - thanks,</div><div class=""><br class=""></div><div class=""> Will.</div><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On 11 May 2016, at 11:07, Jäälinoja, Harri Tapio <<a href="mailto:harri.jaalinoja@helsinki.fi" class="">harri.jaalinoja@helsinki.fi</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" class="" style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;"><div class="" style="margin-top: 0px; margin-bottom: 0px;">Hi,</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">I uploaded some Thermo CellInsight plate data to OMERO 5.2.3, and noticed that there is a problem with the well column index. The wells are numbered A01 -> H12, but OMERO webclient viewer seems to think the index starts from A00, and shifts the wells to the right. Here are some screenshots to show what I mean:</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><a href="https://wiki.helsinki.fi/display/LMU/OMERO+troubleshooting" id="LPlnk943162" title="https://wiki.helsinki.fi/display/LMU/OMERO+troubleshooting
Ctrl+Click or tap to follow the link" class="">https://wiki.helsinki.fi/display/LMU/OMERO+troubleshooting</a><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">In case of a full plate, the right-most column is not shown at all.</div><p class="" style="margin-top: 0px; margin-bottom: 0px;"></p><div class=""><br class=""></div><div class="">hajaalin@dhcp-asv-66:~/tmp$ ls LMU-CELLINSIGHT_151117170001/|head -2</div><div class="">LMU-CELLINSIGHT_151117170001_A01f00d0.C01</div><div class="">LMU-CELLINSIGHT_151117170001_A01f01d0.C01</div><div class="">hajaalin@dhcp-asv-66:~/tmp$ ls LMU-CELLINSIGHT_151117170001/|tail -7</div><div class="">LMU-CELLINSIGHT_151117170001_H12f14d0.C01</div><div class="">LMU-CELLINSIGHT_151117170001_H12f15d0.C01</div><div class=""><br class=""></div><p class="" style="margin-top: 0px; margin-bottom: 0px;"></p><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">As you see in omero_cellomics.png, part of the code has the index right. There "General" tab on the right shows E04 when viewer says E5. Same goes for field index.</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">I have also a feature request related to the viewer: would it be difficult to show a montage of the fields of a given well? It wouldn't even have to be a real stiched image. </div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">Best regards,</div><div class="" style="margin-top: 0px; margin-bottom: 0px;">Harri</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div id="Signature" class=""><div id="divtagdefaultwrapper" class="" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;"><div class="" style="margin-top: 0px; margin-bottom: 0px;">---</div><div class="" style="margin-top: 0px; margin-bottom: 0px;">Harri Jäälinoja</div><div class="" style="margin-top: 0px; margin-bottom: 0px;">Light Microscopy Unit</div><div class="" style="margin-top: 0px; margin-bottom: 0px;">Institute of Biotechnology</div><div class="" style="margin-top: 0px; margin-bottom: 0px;">University of Helsinki</div></div></div></div><span class="" style="font-family: Helvetica; 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