<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Harri-<div><br><div><div>On 7 Oct 2011, at 13:16, Harri Jäälinoja wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><br>Dear Jason,<br><br>this looks very interesting. Would it be possible to display also image analysis results attached to the original images? It would be great to have an easy access to segmentation and/or object recognition results, to have the possibility to check how the analysis has worked.<br><br></div></blockquote><div><br></div><div>We definitely can display ROIs-- identified objects, etc., and these can be linked to features calculated from these images. One of the challenges here is that these are usually fairly custom (even from commercial platforms, there are often many different ways of calculating and storing results). We have achieved this for specific situations.</div><div><br></div><br><blockquote type="cite"><div>Actually I have never seen how the HCS support in OMERO is currently, because OMERO doesn't have readers for our HCS systems. In our unit we have a Cellomics CellInsight and a Leica HCS-A. How is the situation, are there any plans to add support for these? </div></blockquote><div><br></div><div>As always, our support for file formats, via Bio-Formats, depends on great sample data sets. If you have these, we can definitely add it to the Bio-Formats to-do list.</div><br><blockquote type="cite"><div>Both image formats are supported, so that's not a problem. Just the plate level reading is missing. I will have look at the code for the existing HCS readers, but I don't know if I have enough time or skills to implement something.<br></div></blockquote><div><br></div><div>If you mean plate metadata (wells, detectors, channels, etc), that should be straightforward. If you mean analysis results from calculated features, that is certainly more work, and often quite custom. Let us look at the data, and we can tell you what's possible.</div><div><br></div><div>Cheers,</div><div><br></div><div>Jason</div><br><blockquote type="cite"><div><br>Best regards,<br>Harri<br><br><br>On 02/10/11 10:57, Jason Swedlow wrote:<br><blockquote type="cite">Dear All-<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Just an update on our activities with OMERO and HCS data.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">At the beginning of September, the Journal of Cell Biology published<br></blockquote><blockquote type="cite">four HCS screens on the JCB DataViewer (a custom version of OMERO, built<br></blockquote><blockquote type="cite">and maintained by Glencoe Software), totalling about 300 GB of data. The<br></blockquote><blockquote type="cite">first was a genome wide screen of the S. cerevisiae non-essential<br></blockquote><blockquote type="cite">collection, looking for modifiers of the DNA repair pathway. This was<br></blockquote><blockquote type="cite">essentially a "re-publishing" of a previously published paper. The new<br></blockquote><blockquote type="cite">paper is at:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><a href="http://jcb.rupress.org/content/194/5/665">http://jcb.rupress.org/content/194/5/665</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">and the data is at:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><a href="http://jcb-dataviewer.rupress.org/jcb/browse/4608/S1/">http://jcb-dataviewer.rupress.org/jcb/browse/4608/S1/</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Maybe most useful to click on the "Chart" button.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">A second paper, which looked for modifiers of actin structure in cells,<br></blockquote><blockquote type="cite">used one screen in Drosophila cells and two targetted screens in human<br></blockquote><blockquote type="cite">cells: The paper is at:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><a href="http://jcb.rupress.org/content/194/5/789">http://jcb.rupress.org/content/194/5/789</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">and the data is at:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><a href="http://jcb-dataviewer.rupress.org/jcb/browse/4609/">http://jcb-dataviewer.rupress.org/jcb/browse/4609/</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">The presentation of the data there can be debated-- there are advantages<br></blockquote><blockquote type="cite">and disadvantages to what was done, and the decisions were made by many<br></blockquote><blockquote type="cite">people. For example, we think we can do a better job at visualising the<br></blockquote><blockquote type="cite">plates and their content. However, as a scientist, I do like the<br></blockquote><blockquote type="cite">browser-based view of the screen results, that shows what the authors<br></blockquote><blockquote type="cite">scored as hits, and allows me to browse their interpretation of the results.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Data download is enabled at the level of wells (and thus individual<br></blockquote><blockquote type="cite">genes) at the moment. Plate-based data download is coming.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">This custom UI was built by Glencoe Software, under contract to<br></blockquote><blockquote type="cite">Rockefeller University Press. As always, this code is being rolled into<br></blockquote><blockquote type="cite">the GPL-released version of OMERO. We have some versioning issues to<br></blockquote><blockquote type="cite">reconcile, but getting these facilities into the open source codebase is<br></blockquote><blockquote type="cite">a major priority. We'll send updates on this list as the code becomes<br></blockquote><blockquote type="cite">available.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Let us know if you have any questions about this resource, the code or<br></blockquote><blockquote type="cite">our steps going forward.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Cheers,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Jason<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">**************************<br></blockquote><blockquote type="cite">Wellcome Trust Centre for Gene Regulation & Expression<br></blockquote><blockquote type="cite">College of Life Sciences<br></blockquote><blockquote type="cite">MSI/WTB/JBC Complex<br></blockquote><blockquote type="cite">University of Dundee<br></blockquote><blockquote type="cite">Dow Street<br></blockquote><blockquote type="cite">Dundee DD1 5EH<br></blockquote><blockquote type="cite">United Kingdom<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">phone (01382) 385819<br></blockquote><blockquote type="cite">Intl phone: 44 1382 385819<br></blockquote><blockquote type="cite">FAX (01382) 388072<br></blockquote><blockquote type="cite">email: <a href="mailto:jason@lifesci.dundee.ac.uk">jason@lifesci.dundee.ac.uk</a> <<a href="mailto:jason@lifesci.dundee.ac.uk">mailto:jason@lifesci.dundee.ac.uk</a>><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Lab Page: <a href="http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow">http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow</a><br></blockquote><blockquote type="cite">Open Microscopy Environment: <a href="http://openmicroscopy.org">http://openmicroscopy.org</a><br></blockquote><blockquote type="cite">**************************<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">The University of Dundee is a Scottish Registered Charity, No. SC015096.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">ome-devel mailing list<br></blockquote><blockquote type="cite"><a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a><br></blockquote><blockquote type="cite"><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br></blockquote><br><br>-- <br>__________________________________________________<br>Harri Jäälinoja<br>Light Microscopy Unit<br>Institute of Biotechnology, University of Helsinki<br><a href="http://www.biocenter.helsinki.fi/bi/lmu/">http://www.biocenter.helsinki.fi/bi/lmu/</a><br>+358 9 191 59370 fax +358 9 191 59366<br><br>_______________________________________________<br>ome-devel mailing list<br>ome-devel@lists.openmicroscopy.org.uk<br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="font-family: Helvetica; "><br class="Apple-interchange-newline"><br class="khtml-block-placeholder"></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">**************************</span></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">Wellcome Trust Centre for Gene Regulation & Expression</font></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">College of Life Sciences</font></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">MSI/WTB/JBC Complex</font></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">University of Dundee</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Dow Street</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Dundee DD1 5EH</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">United Kingdom</span></div><div style="font-family: Helvetica; "><br style="font-family: Helvetica; "></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">phone (01382) 385819</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Intl phone: 44 1382 385819 </span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">FAX (01382) 388072 </span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">email: <a href="mailto:jason@lifesci.dundee.ac.uk">jason@lifesci.dundee.ac.uk</a></span></div><div style="font-family: Helvetica; "><br style="font-family: Helvetica; "></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Lab Page: </span><a href="http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow">http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow</a></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Open Microscopy Environment: <a href="http://openmicroscopy.org">http://openmicroscopy.org</a></span></div><div style="font-family: Helvetica; ">**************************</div><div style="font-family: Helvetica; "><br class="webkit-block-placeholder"></div><div style="font-family: Helvetica; "><div>The University of Dundee is a Scottish Registered Charity, No. SC015096.</div></div><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"></div></span></span>
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