<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Jason<div class=""><br class=""><div class="">Now I have to plead fatigue or organisational incompetence. I finally clicked on the linked below from your email from Feb 1st. </div><div class="">This is a good demonstration of using figure for a specific study. <br class=""><div class=""><br class="webkit-block-placeholder"></div><div class="">However, I would regard this as a vanilla use of FIGURE. What we are doing is to scale this up to the level of hundreds or thousands of figures. </div><div class="">In otherwords, Figure is the default method of summarising the typical data of any data set you acquire. </div><div class=""><br class=""></div><div class="">Once you reach this scale, it becomes difficult to manage so many figures. The way we are dong so is through using Zegami, as it allows slicing and dicing the figures according to a rich n-dimensional metadata landscape. That way you can explore all the images produced by a group in an instance. </div><div class=""><br class=""></div><div class="">At the moment we have only done this for our smFISH screen in a systematic manner. And we have achieved this through using a strict naming convention for each figure name. Ideally we would like to see better integration into OMERO - so that we for example can export collections of Figures that are themselves tagged in a similar way to the Autotag tool. At the moment we are importing figures through a script that imports all figures with a suffix that constitute a collection (e.g. ending in _zegami1). Not ideal but works. </div><div class=""><br class=""></div><div class="">I hope we can progress these discussions without me or Steve being there. </div><div class=""><br class=""></div><div class="">Regards</div><div class="">Ilan</div><div class=""><br class=""></div><div class=""><br class="webkit-block-placeholder"></div><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: 2; widows: 2;" class=""><div style="font-size: 12px;" class=""><div style="font-size: 18px;" class=""><div style="font-size: 12px;" class=""><span class="Apple-style-span" style="font-size: 18px; border-collapse: separate; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; line-height: normal; border-spacing: 0px;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><div style="font-size: 12px;" class="">____________________________________________________________________________</div><div style="font-size: 12px;" class=""><b class="">Prof. Ilan Davis <a href="mailto:ilan.davis@bioch.ox.ac.uk" class="">ilan.davis@bioch.ox.ac.uk</a> <a href="http://www.ilandavis.com" class="">http://www.ilandavis.com</a></b></div><div class=""><span style="font-size: 12px;" class=""><b class=""><a href="https://twitter.com/ilandavis" class="">https://twitter.com/ilandavis</a></b></span></div><div style="font-size: 12px;" class="">Department of Biochemistry, The University of Oxford, South Parks Road, OXFORD OX1 3QU, UK</div><div style="font-size: 12px;" class="">Direct Office No: (44) (0)1865 613265 Office Fax: (44) (0)1865 613340</div><div style="font-size: 12px;" class="">Lab manager: Dr Darragh Ennis <a href="mailto:darragh.ennis@bioch.ox.ac.uk" class="">darragh.ennis@bioch.ox.ac.uk</a> (44) (0)1865 613271 / 613272 </div><div class=""><span style="font-size: 12px;" class="">PA: </span><span style="text-align: -webkit-auto;" class=""><span style="font-size: 12px;" class=""><a href="mailto:jolanta.parkinson@bioch.ox.ac.uk" class="">jolanta.parkinson@bioch.ox.ac.uk</a> (44) (0)1865 </span></span><span style="text-align: -webkit-auto; font-size: 12px;" class="">613218</span><span style="text-align: -webkit-auto; font-size: 12px;" class=""> </span></div><div style="font-size: 12px;" class="">____________________________________________________________________________</div></div><div style="font-size: 12px;" class=""><br class=""></div></div></span><br class="Apple-interchange-newline" style="font-size: 18px;"></div></div></div></div></div></div></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline">
</div>
<br class=""><div><blockquote type="cite" class=""><div class="">On 1 Feb 2018, at 09:23, Jason Swedlow (Staff) <<a href="mailto:j.r.swedlow@dundee.ac.uk" class="">j.r.swedlow@dundee.ac.uk</a>> wrote:</div><div class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; font-family: Tahoma, Geneva, sans-serif, EmojiFont, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols;" class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; font-family: Tahoma, Geneva, sans-serif, EmojiFont, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols;" class=""><br class=""><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">More to the point-- I definitely should have mentioned OMERO.figure. I was remiss (I plead fatigue and jetlag-- too many meetings in too many timezones). I should have pointed out that all the imaging figures in the Schleicher et al paper were made in OMERO.figure and all of them them are available in the public resource-- go to<span class="Apple-converted-space"> </span><a href="http://dx.doi.org/10.17867/10000109" class="OWAAutoLink" id="LPlnk152923" previewremoved="true">http://dx.doi.org/10.17867/10000109</a>, click on the "Figure" tab, Open File, and under owner select Katharina Schleicher. Not a perfect workflow yet, but getting there. It's critically important that we get your (and others) ideas and use cases for this. So far, the funding panels have not been convinced by OMERO.figure-- we need your help to convince them!</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Cheers,</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Jason<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div id="Signature" class=""><div style="font-family: Tahoma; font-size: 13px;" class=""><div class=""><div class=""><div class=""><div class=""><div style="margin: 0px; font-size: 13px;" class=""><font size="2" class="">----------------------</font></div><div style="margin: 0px; font-size: 13px;" class=""><font size="2" class="">Centre for Gene Regulation & Expression | </font><span style="font-size: small;" class="">Open Microscopy Environment | </span><span style="font-size: small;" class="">University of Dundee </span></div><div style="margin: 0px; font-size: 13px;" class=""><font size="2" class=""><font size="2" class=""><br class=""></font></font></div><div style="margin: 0px; font-size: 13px;" class=""><span style="font-size: small;" class="">Phone: +44 (0) 1382 385819 </span></div><div style="margin: 0px; font-size: 13px;" class=""><font size="2" style="font-size: small;" class="">email: </font><a tabindex="0" href="https://dbxprd0410.outlook.com/owa/redir.aspx?C=XlY__cjOnUCLrUuc7zPnSr5hht0k884Icce5AfHAhv6fHZjWmwxAigQ84T9_MIRi02LghCy2-Tk.&URL=mailto%3aj.swedlow%40dundee.ac.uk" target="_blank" id="LPNoLP" style="font-size: small;" class=""><font size="2" class="">j.swedlow@dundee.ac.uk</font></a></div><div style="margin: 0px; font-size: 13px;" class=""><font size="2" class=""><font size="2" class=""> </font></font></div><div style="margin: 0px; font-size: 13px;" class=""><font size="2" class=""><font size="2" class="">Web: </font><a tabindex="0" href="https://dbxprd0410.outlook.com/owa/redir.aspx?C=XlY__cjOnUCLrUuc7zPnSr5hht0k884Icce5AfHAhv6fHZjWmwxAigQ84T9_MIRi02LghCy2-Tk.&URL=http%3a%2f%2fwww.lifesci.dundee.ac.uk%2fgre%2fstaff%2fjason-swedlow" target="_blank" id="LPNoLP" class=""><font size="2" class="">http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow</font></a></font></div><div style="margin: 0px; font-size: 13px;" class=""><font size="2" class=""><font size="2" class="">Open Microscopy Environment: </font><a tabindex="0" href="https://dbxprd0410.outlook.com/owa/redir.aspx?C=XlY__cjOnUCLrUuc7zPnSr5hht0k884Icce5AfHAhv6fHZjWmwxAigQ84T9_MIRi02LghCy2-Tk.&URL=http%3a%2f%2fopenmicroscopy.org" target="_blank" id="LPNoLP" class=""><font size="2" class="">http://openmicroscopy.org</font></a></font></div><div style="margin: 0px; font-family: Tahoma; font-size: 13px;" class=""><font size="2" face="Helvetica" class=""><br class=""></font></div></div></div></div></div></div></div></div><hr tabindex="-1" style="display: inline-block; width: 1477.828125px;" class=""><div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>ome-devel <<a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk" class="">ome-devel-bounces@lists.openmicroscopy.org.uk</a>> on behalf of Ilan Davis <<a href="mailto:ilandavis@mac.com" class="">ilandavis@mac.com</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>01 February 2018 07:33:27<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>OME External Developer List; King Charles House; <a href="mailto:darragh.ennis@bioch.ox.ac.uk" class="">darragh.ennis@bioch.ox.ac.uk</a>; Richard Parton; David Pinto<br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ome-devel] Updates on Data Publication</font><div class=""> </div></div><div dir="auto" class=""><div class=""><span class=""></span></div><div class="">Hi Jason<div class=""><br class=""><div class="">This is great and thanks for the update. Also congrats on your very nice paper in open bio. </div><div class=""><br class=""></div><div class="">I wonder whether you considered ways to include Figure as an option within the publication process. My lab now has a general system in place that people use Figure very effectively as a device to summarise “typical” data from each data set. This is an important shortcut to browse your own data and that of others and be able to record what people think is a correct summary of a data set. </div><div class=""><br class=""></div><div class="">In other words, publishing the original data transparently should be part of the publication process and your example in the open bio paper is great. It would also be good to be able to publish the figures in a paper as OMERO Figures that map each panel to the exact original data - as it does anyway at the moment. </div><div class=""><br class=""></div><div class="">Can that be achieved already with the existing omero server infrastructure? Can figure be integrated in some way within the IDR infrustructure so IDR can be used to publish data from individual low throughout papers as well as high throughout studies with the figures providing a high level Quick view and guide to the data?</div><div class=""><br class=""></div><div class="">Thanks</div><div class="">Regards</div><div class="">Ilan</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div id="x_AppleMailSignature" class="">Sent from my iPhone</div><div class=""><br class="">On 1 Feb 2018, at 01:46, Jason Swedlow (Staff) <<a href="mailto:j.r.swedlow@dundee.ac.uk" class="">j.r.swedlow@dundee.ac.uk</a>> wrote:<br class=""><br class=""></div><blockquote type="cite" class=""><div class=""><div class="x_WordSection1"><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span lang="EN-US" style="font-size: 11pt;" class="">Dear All<span class="Apple-converted-space"> </span></span></div><p class="x_MsoNormal" style="margin-top: 0px; margin-bottom: 0px;"><span lang="EN-US" style="font-size: 11pt;" class=""> </span></p><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span lang="EN-US" style="font-size: 11pt;" class="">Just a quick update on our recent activities in data publication.</span></div><p class="x_MsoNormal" style="margin-top: 0px; margin-bottom: 0px;"><span lang="EN-US" style="font-size: 11pt;" class=""> </span></p><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span lang="EN-US" style="font-size: 11pt;" class="">IDR continues to receive datasets, and we have several exciting new datasets upcoming. Keep an eye on the announcements and let us know if you have a reference dataset that should be in IDR. See<span class="Apple-converted-space"> </span><a href="https://idr.openmicroscopy.org/about/submission.html" class="">https://idr.openmicroscopy.org/about/submission.html</a>.</span></div><p class="x_MsoNormal" style="margin-top: 0px; margin-bottom: 0px;"><span lang="EN-US" style="font-size: 11pt;" class=""> </span></p><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span lang="EN-US" style="font-size: 11pt;" class="">OME, as it always has, wants to make data publication from individual laboratories routine. That’s one of the big reasons to use OMERO in a lab or research institute. We’ve worked hard to make the process for publishing data easier in OMERO 5.4, and also better documented. We used OMERO 5.4’s features to publish data associated with a paper from our lab (some of you will correctly recognize this as a dogfooding exercise). The paper is at<a href="http://doi.org/10.1098/rsob.170099" class="">http://doi.org/<span lang="EN-GB" class="">10.1098/rsob.170099</span></a></span><span lang="EN-US" style="font-size: 11pt;" class="">,</span><span lang="EN-US" style="font-size: 11pt;" class=""><span class="Apple-converted-space"> </span>and the original image data is at<span class="Apple-converted-space"> </span></span><span style="font-size: 11pt;" class=""><a href="http://dx.doi.org/10.17867/10000109" class="">http://dx.doi.org/10.17867/10000109</a></span><span lang="EN-US" style="font-size: 11pt;" class="">. For more info, see our recent entry on the OME Blog (<a href="http://blog.openmicroscopy.org/community/2018/01/25/fair/" class="">http://blog.openmicroscopy.org/community/2018/01/25/fair/</a>).</span><span style="font-size: 11pt;" class=""></span></div><p class="x_MsoNormal" style="margin-top: 0px; margin-bottom: 0px;"><span lang="EN-US" style="font-size: 11pt;" class=""> </span></p><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span lang="EN-US" style="font-size: 11pt;" class="">And finally, we’ve contributed to a white paper that discusses the resources the community must (at least we think it must) build to make image data publication routine and universal. This is now on arxiv at<span class="Apple-converted-space"> </span><a href="https://arxiv.org/abs/1801.10189" class="">https://arxiv.org/abs/1801.10189</a> (it’s on arxiv because bioRxiv doesn't publish proposals and white papers; yes we did try to put it there first!).</span></div><p class="x_MsoNormal" style="margin-top: 0px; margin-bottom: 0px;"><span lang="EN-US" style="font-size: 11pt;" class=""> </span></p><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span lang="EN-US" style="font-size: 11pt;" class="">As always, we welcome your thoughts, comments, critiques, and ideas.</span></div><p class="x_MsoNormal" style="margin-top: 0px; margin-bottom: 0px;"><span lang="EN-US" style="font-size: 11pt;" class=""> </span></p><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span lang="EN-US" style="font-size: 11pt;" class="">Cheers,</span></div><p class="x_MsoNormal" style="margin-top: 0px; margin-bottom: 0px;"><span lang="EN-US" style="font-size: 11pt;" class=""> </span></p><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span lang="EN-US" style="font-size: 11pt;" class="">Jason</span></div><p class="x_MsoNormal" style="margin-top: 0px; margin-bottom: 0px;"><span lang="EN-US" style="font-size: 11pt;" class=""> </span></p><p class="x_MsoNormal" style="margin-top: 0px; margin-bottom: 0px;"><span lang="EN-US" style="font-size: 11pt;" class=""> </span></p></div><br class=""><span style="font-size: 10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span></div></blockquote><blockquote type="cite" class=""><div class=""><span class="">_______________________________________________</span><br class=""><span class="">ome-devel mailing list</span><br class=""><span class=""><a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.openmicroscopy.org.uk</a></span><br class=""><span class=""><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a></span><br class=""></div></blockquote></div></div></div></div></div><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span><span style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class=""><span class="Apple-converted-space"> </span>_______________________________________________</span><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">ome-devel mailing list</span><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="mailto:ome-devel@lists.openmicroscopy.org.uk" style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">ome-devel@lists.openmicroscopy.org.uk</a><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a></div></blockquote></div><br class=""></div></div></body></html>