<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></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=""> 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><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" 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="">it's the same in Insight client:</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><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 style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I uploaded a full plate, one field per well, about 20MB.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Thanks!</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Harri<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><img src="https://wiki.helsinki.fi/display/LMU/OMERO+troubleshooting?preview=/196947403/196949286/omeroi_cellomics.png" class=""></div><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p></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: 792.8125px;" 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 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 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 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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