<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 Will <div class="">thanks for all your efforts</div><div class="">We have met today and they filled me in with the tools and what can be done with parade. Sounds good. We will need to trial it once parade is installed and test how it works for our scientific needs. </div><div class="">We will keep the conversation going. </div><div class="">regards</div><div class="">ilan<br class=""><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 7 Jun 2018, at 13:52, William Moore (Staff) <<a href="mailto:W.Moore@dundee.ac.uk" class="">W.Moore@dundee.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi Josh,
<div class=""><br class="">
</div>
<div class=""> Great. So how well does this set-up work for you to organise figures (images-of-figures) in the webclient?</div>
<div class=""><br class="">
</div>
<div class="">I guess you may need to try Parade before you can test the full filtering options.</div>
<div class=""><br class="">
</div>
<div class=""> Cheers,</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 6 Jun 2018, at 15:32, Joshua S Titlow <<a href="mailto:joshua.titlow@bioch.ox.ac.uk" class="">joshua.titlow@bioch.ox.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">The script works as advertised.
<div class="">Thanks Will!<br class="">
</div>
<div class="">j</div>
<div class="gmail_extra">
<div class="">
<div class="gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr" class="">
<div dir="ltr" class="">
<div dir="ltr" class=""><br class="">
</div>
</div>
</div>
</div>
</div>
<br class="">
<div class="gmail_quote">On Tue, Jun 5, 2018 at 4:30 PM, William Moore (Staff) <span dir="ltr" class="">
<<a href="mailto:W.Moore@dundee.ac.uk" target="_blank" class="">W.Moore@dundee.ac.uk</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">
<div class=""><br class="">
</div>
Hi Josh (T),
<div class=""><br class="">
</div>
<div class=""> I wrote a little script that will take the sample tab-separated-value text-file you gave us and use it to add</div>
<div class="">Map Annotations and Tags in OMERO.</div>
<div class=""><a href="https://gist.github.com/will-moore/8b6575c279ea3fdc3aff4c84e803056e" target="_blank" class="">https://gist.github.com/will-<wbr class="">moore/<wbr class="">8b6575c279ea3fdc3aff4c84e80305<wbr class="">6e</a></div>
<div class=""><br class="">
</div>
<div class="">If you have a Dataset with images within it that correspond to the names in the “image” column of your table and run</div>
<div class="">this script with the Dataset ID, it will create a Map Annotation with all the row data for that Image.</div>
<div class=""><br class="">
</div>
<div class="">Links to figure etc are clickable and you can filter by all the map annotations in OMERO.parade, which works nicely.</div>
<div class=""><br class="">
</div>
<div class="">However, when you choose to filter by e.g. Gene, you’re not given a list of genes to choose from in Parade (you just have to</div>
<div class="">type in Gene names to filter).</div>
<div class=""><br class="">
</div>
<div class="">So, I also added some lines to create a Tag from each Gene name.</div>
<div class="">This gives you the ability to filter by Gene (Tag), which is also well-supported in webclient without needing Parade.</div>
<div class=""><br class="">
</div>
<div class="">I also add the URL to figure in the Image Description.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Give it a try and let us know what works for you.</div>
<div class="">Hopefully you can get Parade installed somewhere to try out, but even without it, you can do the filtering by Gene.</div>
<div class=""><br class="">
</div>
<div class="">The TSV to Map-Annotation code could be turned into a general-purpose OMERO script since it is quite generic.</div>
<div class="">(needs to support CSV too first).</div>
<div class=""><br class="">
</div>
<div class="">Then other users could run this script on TSV/CSV files they’ve added to a Dataset (similar to populate_metadata.py)</div>
<div class="">without needing to run script client-side.</div>
<div class=""><br class="">
</div>
<div class=""> Cheers,</div>
<div class=""><br class="">
</div>
<div class=""> Will.</div>
<div class="">
<div class="h5">
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 5 Jun 2018, at 11:27, William Moore (Staff) <<a href="mailto:W.Moore@dundee.ac.uk" target="_blank" class="">W.Moore@dundee.ac.uk</a>> wrote:</div>
<br class="m_1718352761905303641Apple-interchange-newline">
<div class="">
<div style="word-wrap:break-word" class="">
<div class="">Hi Ilan,</div>
<div class=""><br class="">
</div>
<div class="">Jean-Marie and I had a good discussion with Josh and MK at the OME meeting. I think we have a good understanding of what’s needed now.</div>
<div class=""><br class="">
</div>
<div class="">To summarise the discussion / feature-requests so far:</div>
<div class=""> - Need to be able to organise figures in much the same way as Images: Tag, Project/Dataset (or Folder?) and also to filter by metadata (as in OMERO.parade).</div>
<div class=""> - Various export features (e.g. export all figures with a certain Tag, export as png etc) but not sure how important these are if everything happens within OMERO (no export to Zegami)?</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">In order for the webclient to organise figures, we could try to improve the handling of Files (File-Annotations) which are supported better in Insight.</div>
<div class="">However, to do this as well as is currently supported for Images would be a huge amount of work. Also, we’d still miss a visual representation of each Figure. Browsing the figure JSON files without any thumbnail or view of the figure would be
tricky.</div>
<div class=""><br class="">
</div>
<div class="">I believe the solution is to export figures to create Images in OMERO, so that every figure is also represented as an OMERO Image.</div>
<div class="">These images can then be organised as desired into Datasets, Tagged or annotated with Key-Value pairs (Map Annotations) and/or assigned attributes in OMERO.tables.</div>
<div class="">This means that we don’t need to organise/tag/manage the actual Figure files - we simply use the existing webclient functionality for managing Images, and each Image-of-a-figure links to the figure itself.</div>
<div class=""><br class="">
</div>
<div class="">We can already export figures to Images in OMERO, so the first steps will be to help you to adopt this workflow, either starting with figures where you’ve previously exported pngs for zegami, or with new figures.</div>
<div class="">We can also start to design the changes that are needed to facilitate this workflow for other users, to make it the standard way of organising figures in OMERO.</div>
<div class=""><br class="">
</div>
<div class="">First Steps (starting with previously exported pngs):</div>
<div class=""><br class="">
</div>
<div class="">If you have a collection of pngs in a directory, you can import them all into a single Dataset (ID 123), either via command line:</div>
<div class="">$ bin/omero import -d 123 path/to/directory/</div>
<div class="">or via Insight.</div>
<div class="">Then, use a Python script to parse the text file that Zegami uses and for each row in the table:</div>
<div class=""> - find the imported png in the Dataset by name, and add the URL to figure in its description</div>
<div class=""> - use other metadata in the text file to add Map annotations to the image for searching/filtering</div>
<div class=""><br class="">
</div>
<div class="">Now you should be able to use OMERO.parade to do similar searches and filtering as you have been doing in Zegami.</div>
<div class=""><br class="">
</div>
<div class="">First Steps (starting with figures not yet exported):</div>
<div class=""><br class="">
</div>
<div class="">If you need to batch export figures, you can use David’s script with “OMERO” as the export option. TODO:</div>
<div class=""> - We need to add the Figure URL to the description of new images, so that we can link back to the figure from the image.</div>
<div class=""> - We need a ‘Dataset_IDs’ parameter to save the figure to chosen Dataset(s) (we had this working already at the OME meeting).</div>
<div class=""> - Then we’d need some way to add the map annotations as above. If you have these in a CSV file already, then simply use the same script as above. Or use a script that could create map annotations directly from data read from FlyMine?</div>
<div class=""> - Ideally we could make this process accessible to users without needing a developer to run scripts. E.g. if they know the Gene name, they could run a server-side script to create all the map annotations from this (getting data from FlyMine)
etc.</div>
<div class=""><br class="">
</div>
<div class="">The main remaining issue would be how to update the exported Image in OMERO when the figure changes. Initially you could repeat the initial export (add annotations etc) and simply delete the previously created Image.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Workflow improvement:</div>
<div class=""><br class="">
</div>
<div class="">Once we are happy that the basic idea of each Figure linked to an Image-of-a-Figure is a valid way to organise your figures,</div>
<div class="">we can look to improve the workflow for other users. There are several new features needed, but</div>
<div class="">instead of adding to this e-mail, I’ve moved these to a design issue at <a href="https://github.com/openmicroscopy/design/issues/96" target="_blank" class="">https://github.com/<wbr class="">openmicroscopy/design/issues/<wbr class="">96</a> </div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""> Regards,</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>
<div class="">
<blockquote type="cite" class="">
<div class="">On 22 May 2018, at 21:45, Ilan Davis <<a href="mailto:ilandavis@me.com" target="_blank" class="">ilandavis@me.com</a>> wrote:</div>
<br class="m_1718352761905303641Apple-interchange-newline">
<div class="">
<div style="word-wrap:break-word" class="">Hi Jason
<div class=""><br class="">
</div>
<div class="">thanks. I guess I will answer this a bit philosophically or strategically, </div>
<div class="">We are developing this ourselves, but my strong feeling is that we cannot really do a proper job of creating very good tools in the way we are doing it by patching our way between two non intra-operable systems and also without getting into the
guts of the OMERO code. </div>
<div class=""><br class="">
</div>
<div class="">I also think it is wrong to think of our workflows as specialised ones for a particular one off purpose. They are workflows that should be adopted by virtually all cell biology labs that I know of. Have you surveyed how people are using OMERO
in non-specialist labs? </div>
<div class=""><br class="">
</div>
<div class="">The way I see it, and perhaps failing to explain it properly, is that what we are doing is creating a general purpose workflow that should be a next-generation way of dealing with data transparently within a team. The team and individuals can
define a way to browse their data that contains implicit information in its organisation and metadata and collection of panels and choice of “typical data” that allow members of teams to understand each others data. It also allows users to accumulate over
time a history of the meaning of their data, as they acquire it bit by bit. So my PhD students for example, essentially have their figures made for their thesis as they go along. </div>
<div class=""><br class="">
</div>
<div class="">I realise it maybe hard to grasp what I am talking about, as this is a bit of a sociological / anthropological point. It is not a revolutionary scientific idea. It is a workflow that I think everyone should adopt as standard. I suspect that eventually
this will be considered mandatory for data transparency and integrity. Just having a collection of raw data is good, but not sufficient. </div>
<div class=""><br class="">
</div>
<div class="">Strategically, from the point of view of the OMERO project using a work flow of this sort, would make the whole project adoptable by everyone who does microscopy rather than just the more advanced users with particularly skilled staff. </div>
<div class=""><br class="">
</div>
<div class="">I am convinced that the OMERO team can create a better work flow than we can for a base level method of making all data that everyone acquires (not only high content screens) transparent and understandable by anyone. </div>
<div class=""><br class="">
</div>
<div class="">I will respond to Will’s helpful and useful comments separately, as they are much more specific. </div>
<div class=""><br class="">
</div>
<div class="">Regards</div>
<div class="">ilan</div>
<div class=""><br class="">
</div>
<div class="">ps As steve and I will not be there, perhaps you (and Will and Josh M) can schedule time with Josh and MK to go through the wokflow, the scripts (that Steve wrote and Josh modified) as well as see the cloud version of Zegami in operation. I think
it is easier to understand my point above by just seeing examples. </div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word" class="">
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word" class="">
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word" class="">
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word" class="">
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word" class="">
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word" class="">
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word" class="">
<div class="">
<div style="font-size:12px" class="">
<div style="font-size:18px" class="">
<div style="font-size:12px" class=""><span class="m_1718352761905303641Apple-style-span" style="font-size:18px;border-collapse:separate;border-spacing:0px">
<div style="word-wrap:break-word" class="">
<div class="">
<div style="font-size:12px" class="">______________________________<wbr class="">______________________________<wbr class="">________________</div>
<div style="font-size:12px" class=""><b class="">Prof. Ilan Davis <a href="mailto:ilan.davis@bioch.ox.ac.uk" target="_blank" class="">ilan.davis@bioch.ox.ac.uk</a>
<a href="http://www.ilandavis.com/" target="_blank" class="">http://www.ilandavis.com</a></b></div>
<div class=""><span style="font-size:12px" class=""><b class=""><a href="https://twitter.com/ilandavis" target="_blank" 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" target="_blank" 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" target="_blank" class="">jolanta.parkinson@bioch.ox.<wbr class="">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="">______________________________<wbr class="">______________________________<wbr class="">________________</div>
</div>
<div style="font-size:12px" class=""><br class="">
</div>
</div>
</span><br class="m_1718352761905303641Apple-interchange-newline" style="font-size:18px">
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br class="m_1718352761905303641Apple-interchange-newline">
</div>
<br class="m_1718352761905303641Apple-interchange-newline">
</div>
<br class="m_1718352761905303641Apple-interchange-newline">
</div>
<br class="m_1718352761905303641Apple-interchange-newline">
</div>
<br class="m_1718352761905303641Apple-interchange-newline">
<br class="m_1718352761905303641Apple-interchange-newline">
</div>
<br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 22 May 2018, at 19:30, Jason Swedlow (Staff) <<a href="mailto:j.r.swedlow@dundee.ac.uk" target="_blank" class="">j.r.swedlow@dundee.ac.uk</a>> wrote:</div>
<br class="m_1718352761905303641Apple-interchange-newline">
<div class="">
<div class="m_1718352761905303641WordSection1" 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">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="m_1718352761905303641EmailStyle19" style="font-family:Calibri,sans-serif;color:windowtext">Hi Ilan<u class=""></u><u class=""></u></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="m_1718352761905303641EmailStyle19" style="font-family:Calibri,sans-serif;color:windowtext"> </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="m_1718352761905303641EmailStyle19" style="font-family:Calibri,sans-serif;color:windowtext">My €$£0.02.<u class=""></u><u class=""></u></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="m_1718352761905303641EmailStyle19" style="font-family:Calibri,sans-serif;color:windowtext"> </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="m_1718352761905303641EmailStyle19" style="font-family:Calibri,sans-serif;color:windowtext">We really appreciate all these comments. As you will have seen, we just released OMERO.figure 4.0, where we add support for “big” images (really large X-Y
planes), which has been requested over and over again and required a lot of work to get right (or at least roughly so). <span class="m_1718352761905303641Apple-converted-space"> </span><u class=""></u><u class=""></u></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="m_1718352761905303641EmailStyle19" style="font-family:Calibri,sans-serif;color:windowtext"> </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="m_1718352761905303641EmailStyle19" style="font-family:Calibri,sans-serif;color:windowtext">The broader point of putting Figures under management in a serious way is a very important point. Your lab clearly has some very interesting workflows, and
I look forward to hearing more about them at the upcoming Users Meeting. The whole point of an open project is people take technology in all sorts of ways that we won’t have thought of. As Will stated, a few of these are on the list, and several others are
new ideas—so thank you!!!<u class=""></u><u class=""></u></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="m_1718352761905303641EmailStyle19" style="font-family:Calibri,sans-serif;color:windowtext"> </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="m_1718352761905303641EmailStyle19" style="font-family:Calibri,sans-serif;color:windowtext">We’ll discuss at the upcoming Users meeting, take in more feedback, and come up with a plan for taking these forward.<u class=""></u><u class=""></u></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="m_1718352761905303641EmailStyle19" style="font-family:Calibri,sans-serif;color:windowtext"> </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="m_1718352761905303641EmailStyle19" style="font-family:Calibri,sans-serif;color:windowtext">Huge thanks again.<u class=""></u><u class=""></u></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="m_1718352761905303641EmailStyle19" style="font-family:Calibri,sans-serif;color:windowtext"> </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="m_1718352761905303641EmailStyle19" style="font-family:Calibri,sans-serif;color:windowtext">Cheers,<u class=""></u><u class=""></u></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="m_1718352761905303641EmailStyle19" style="font-family:Calibri,sans-serif;color:windowtext"> </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="m_1718352761905303641EmailStyle19" style="font-family:Calibri,sans-serif;color:windowtext">Jason<u class=""></u><u class=""></u></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<u class=""></u> <u class=""></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<u class=""></u> <u class=""></u></div>
<div style="border-style:solid none none;border-top-width:1pt;border-top-color:rgb(181,196,223);padding:3pt 0cm 0cm" class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<b class=""><span style="font-size:12pt" class="">From:<span class="m_1718352761905303641Apple-converted-space"> </span></span></b><span style="font-size:12pt" class="">William Moore <<a href="mailto:W.Moore@dundee.ac.uk" target="_blank" class="">W.Moore@dundee.ac.uk</a>><br class="">
<b class="">Date:<span class="m_1718352761905303641Apple-converted-space"> </span></b>Tuesday, 22 May 2018 at 15:41<br class="">
<b class="">To:<span class="m_1718352761905303641Apple-converted-space"> </span></b>OME Development <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank" class="">ome-devel@lists.<wbr class="">openmicroscopy.org.uk</a>><br class="">
<b class="">Cc:<span class="m_1718352761905303641Apple-converted-space"> </span></b>Jason Swedlow <<a href="mailto:j.r.swedlow@dundee.ac.uk" target="_blank" class="">j.r.swedlow@dundee.ac.uk</a>>, Joshua Titlow <<a href="mailto:joshua.titlow@bioch.ox.ac.uk" target="_blank" class="">joshua.titlow@bioch.ox.ac.uk</a>><wbr class="">,
mkaythomp_gmail_com <<a href="mailto:mkaythomp@gmail.com" target="_blank" class="">mkaythomp@gmail.com</a>>, Darragh Ennis <<a href="mailto:darragh.ennis@bioch.ox.ac.uk" target="_blank" class="">darragh.ennis@bioch.ox.ac.uk</a>><wbr class="">, Richard Parton
<<a href="mailto:richard.parton@bioch.ox.ac.uk" target="_blank" class="">richard.parton@bioch.ox.ac.uk</a><wbr class="">>, David Susano Pinto <<a href="mailto:david.pinto@bioch.ox.ac.uk" target="_blank" class="">david.pinto@bioch.ox.ac.uk</a>><br class="">
<b class="">Subject:<span class="m_1718352761905303641Apple-converted-space"> </span></b>Re: [ome-devel] Request for feature development for FIGURE - for discussion by the community<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<u class=""></u> <u class=""></u></div>
</div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<a name="m_1718352761905303641__MailOriginalBody" class="">Hi Illan, <span class="m_1718352761905303641Apple-converted-space"> </span><u class=""></u><u class=""></u></a></div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> Thanks for the all the feedback.<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">It’s great to hear that OMERO.figure is being so useful for you and to get a clear idea of what improvements are needed.<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">I’ll respond to the various requests below in-line...<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
<div class="">
<blockquote style="margin-top:5pt;margin-bottom:5pt" type="cite" class="">
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">On 16 May 2018, at 16:30, Ilan Davis <</span><a href="mailto:ilan.davis@bioch.ox.ac.uk" style="color:purple;text-decoration:underline" target="_blank" class=""><span class="">ilan.davis@bioch.ox.ac.uk</span><span class=""></span></a><span class="">>
wrote:<u class=""></u><u class=""></u></span></div>
</div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
<div class="">
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">Dear OME developer community<u class=""></u><u class=""></u></span></div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">We love OMERO-figure. It has become a central way we use OMERO and we believe it is an under appreciated tool that everyone should use for all their day to day imaging. We would like to see the OMERO team embracing this and putting a small amount
of effort in getting it even better. Please please please put these request high up on a priority list…<u class=""></u><u class=""></u></span></div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""><b class="">Motivation</b></span><span class=""><u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">Figure was developed to make it possible to make figures for papers directly from OMERO and bypassing illustrator and the like. <u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">However, for us it has enabled an unintended additional use that we believe is more significant. It allows every time a user has an imaging session on a microscope to summarise the typical result of that session. It also allows a systematic record
of a medium scale screen, again summarising how the user thinks the data should be viewed. Viewing raw data from a screen is rather difficult in comparison. We have been using Zegami, as a visualisation tool that can organise and slice and dice the figures
at scale using rich n-dimensional meta-data of our choice including bioinformatics. <u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">The following are specific requests framed in general terms and have mostly been posted previously over an extended period by various members of my group and Micron in Oxford. David Pinto, Josh Titlow, MK Thompson will be at the next OMERO meeting
in Dundee and can discuss these points in more detail. <u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""><b class="">Development requests</b></span><span class=""><u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">1) Make some small improvements to Figure so it is sufficient for making figures for papers (other than drawing diagrams and plots). e.g. scalable text and better text labels. Does not have to be extensive and complex. Just one labelling approach
that is good. <u class=""></u><u class=""></u></span></div>
</div>
</div>
</div>
</div>
</blockquote>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">We have an existing feature request for “Stand-alone labels” (labels that can be placed anywhere on the page)<span class="m_1718352761905303641Apple-converted-space"> </span></span><a href="https://trello.com/c/wtu7IVuN/10-stand-alone-labels" style="color:purple;text-decoration:underline" target="_blank" class=""><span class="">https://trello.com/c/<wbr class="">wtu7IVuN/10-stand-alone-labels</span><span class=""></span></a><span class=""><wbr class="">. <u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">Does this cover your needs or are there other improvements to the existing panel labels that you’d like to see?<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">You can set font-sizes on labels already. Does “scalable text” include some other functionality or more flexible sizes?<u class=""></u><u class=""></u></span></div>
</div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""><br class="">
<br class="">
<u class=""></u><u class=""></u></span></div>
<blockquote style="margin-top:5pt;margin-bottom:5pt" type="cite" class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">2) Create a hierarchy of folders housing figures so that figures can be organised in a sensible way over time, at scale. <u class=""></u><u class=""></u></span></div>
</div>
</div>
</div>
</div>
</blockquote>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""><br class="">
The folders feature request is listed at<span class="m_1718352761905303641Apple-converted-space"> </span></span><a href="https://trello.com/c/LwAVYUjm/165-save-figures-in-folders" style="color:purple;text-decoration:underline" target="_blank" class=""><span class="">https://trello.com/c/<wbr class="">LwAVYUjm/165-save-figures-in-<wbr class="">folders</span><span class=""></span></a><span class=""> with
some discussion as to options and timescale<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">(which is currently limited by the OMERO model for Folders - so this needs to change first in OMERO).<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<blockquote style="margin-top:5pt;margin-bottom:5pt" type="cite" class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">3) Use some kind of tagging system, similar to Auto-tag (or repurpose the Auto-tag code) - extracting tags from the folder and figure names. <u class=""></u><u class=""></u></span></div>
</div>
</div>
</div>
</div>
</blockquote>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">A tagging system would consist of 2 main features.<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">- ‘Add Tags’ dialog/panel - similar to that in webclient, and/or extend Auto-Tag (if users have lots of tokens in their figure names).<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">- Browse Tag hierarchy from within the figure app.<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">This could be a fair bit of work to do this properly (e.g. webclient Tag dialog is quite complex, so is webtagging). If we had “folders for figures”, would you still want Tagging for figures? Do you need both?<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">NB: currently webclient (or Tag-searcher) will not display Tagged File-Annotations (figures).<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">Card created at </span><a href="https://trello.com/c/X2lvut2c/192-add-tags-to-figures-browse-by-tag" style="color:purple;text-decoration:underline" target="_blank" class=""><span class="">https://trello.com/c/<wbr class="">X2lvut2c/192-add-tags-to-<wbr class="">figures-browse-by-tag</span><span class=""></span></a><span class=""> <u class=""></u><u class=""></u></span></div>
</div>
</div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""><br class="">
<br class="">
<u class=""></u><u class=""></u></span></div>
<blockquote style="margin-top:5pt;margin-bottom:5pt" type="cite" class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">4) Allow batch export of figures from pull down menus as well as CLI. At the moment we are pulling the figures from json files using our own bespoke python scripts. <u class=""></u><u class=""></u></span></div>
</div>
</div>
</div>
</div>
</blockquote>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">Batch export of Figures was previously being discussed at<span class="m_1718352761905303641Apple-converted-space"> </span></span><a href="https://github.com/ome/omero-figure/issues/151" style="color:purple;text-decoration:underline" target="_blank" class=""><span class="">https://github.com/ome/<wbr class="">omero-figure/issues/151</span><span class=""></span></a><span class=""> (Josh
Titlow).<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">However, one of the main issues has been identified by David Pinto<span class="m_1718352761905303641Apple-converted-space"> </span></span><a href="https://github.com/ome/omero-figure/issues/289" style="color:purple;text-decoration:underline" target="_blank" class=""><span class="">https://github.com/ome/<wbr class="">omero-figure/issues/289</span><span class=""></span></a><span class=""> which
is the fact that the export creates a File Annotation on OMERO.<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">We really need to split the Figure Export functionality out of the Figure_To_Pdf.py script so that we can generate figures directly from Python without requiring the scripting service. Some of that work was started at<span class="m_1718352761905303641Apple-converted-space"> </span></span><a href="https://github.com/ome/omero-figure/pull/240" style="color:purple;text-decoration:underline" target="_blank" class=""><span class="">https://github.com/ome/<wbr class="">omero-figure/pull/240</span><span class=""></span></a><span class=""> to
allow the web app to generate figures without the Scripting service. I abandoned this when it became clear that this wouldn’t work from the web, but it would still be useful in your case (and others) to allow batch exports etc.<u class=""></u><u class=""></u></span></div>
</div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""><br class="">
<br class="">
<u class=""></u><u class=""></u></span></div>
<blockquote style="margin-top:5pt;margin-bottom:5pt" type="cite" class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">5) Allow more format of figure export especially .png<u class=""></u><u class=""></u></span></div>
</div>
</div>
</div>
</div>
</blockquote>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">PNG export should be quite straightforward to implement. Created card at<span class="m_1718352761905303641Apple-converted-space"> </span></span><a href="https://trello.com/c/N0PQjMKJ/189-export-as-png" style="color:purple;text-decoration:underline" target="_blank" class=""><span class="">https://trello.com/c/<wbr class="">N0PQjMKJ/189-export-as-png</span><span class=""></span></a><span class=""> <u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""><br class="">
<br class="">
<u class=""></u><u class=""></u></span></div>
<blockquote style="margin-top:5pt;margin-bottom:5pt" type="cite" class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">6) Ideally export metadata with the figures including the tags and automate publishing of figure collections through Zegami with metadata (via .png and csv files). <u class=""></u><u class=""></u></span></div>
</div>
</div>
</div>
</div>
</blockquote>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">Is there particular metadata other than Tags you’d like to export? Exporting an extra csv file would require export of a zip instead of PDF/TIFF, which would complicate<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">the workflow a bit and we’d probably want to make it optional in that case.<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">It may be that the best option here is to create a custom Python script that exports all the metadata you want in a format of your choice. <u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">This gives you the most flexibility and can be updated according to your needs without the UI and workflow changes for other users.<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> Thanks again for your input.<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> I look forward to more discussions at the OME meeting next week,<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> Regards,<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> Will.<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">PS. Another release of OMERO.figure just went out today: </span><a href="http://www.openmicroscopy.org/2018/05/22/figure-4-0-0.html" style="color:purple;text-decoration:underline" target="_blank" class=""><span class="">http://www.<wbr class="">openmicroscopy.org/2018/05/22/<wbr class="">figure-4-0-0.html</span><span class=""></span></a><span class=""><u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<blockquote style="margin-top:5pt;margin-bottom:5pt" type="cite" class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">I welcome comments, clarifications, questions or counterpoints. <u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">with best regards<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">Ilan<u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""><b class="">For transparency:</b></span><span class=""><u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""><b class="">I am on the SAB of Zegami and on the SAB of OMERO-IDR</b></span><span class=""><u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">p.s.If you would like to know more about Zegami, please look up. </span><a href="https://zegami.com/" style="color:purple;text-decoration:underline" target="_blank" class=""><span class="">https://zegami.com/</span><span class=""></span></a><span class=""><u class=""></u><u class=""></u></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
<div class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""><span style="font-size:9pt" class="">______________________________<wbr class="">______________________________<wbr class="">________________<u class=""></u><u class=""></u></span></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""><b class=""><span style="font-size:9pt" class="">Prof. Ilan Davis </span></b></span><a href="mailto:ilan.davis@bioch.ox.ac.uk" style="color:purple;text-decoration:underline" target="_blank" class=""><span class=""><b class=""><span style="font-size:9pt" class="">ilan.davis@bioch.ox.ac.uk</span></b></span><span class=""></span></a><span class=""><b class=""><span style="font-size:9pt" class=""><span class="m_1718352761905303641Apple-converted-space"> </span> <span class="m_1718352761905303641Apple-converted-space"> </span></span></b></span><a href="http://www.ilandavis.com/" style="color:purple;text-decoration:underline" target="_blank" class=""><span class=""><b class=""><span style="font-size:9pt" class="">h<wbr class="">ttp://www.ilandavis.com</span></b></span><span class=""></span></a><span class=""><span style="font-size:9pt" class=""><u class=""></u><u class=""></u></span></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""></span><a href="https://twitter.com/ilandavis" style="color:purple;text-decoration:underline" target="_blank" class=""><span class=""><b class=""><span style="font-size:9pt" class="">https://twitter.com/ilandavis</span></b></span><span class=""></span></a><span class=""><span style="font-size:13.5pt" class=""><u class=""></u><u class=""></u></span></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""><span style="font-size:9pt" class="">Department of Biochemistry, The University of Oxford, South Parks Road, OXFORD OX1 3QU, UK<u class=""></u><u class=""></u></span></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""><span style="font-size:9pt" class="">Direct Office No: (44) (0)1865 613265 Office Fax: (44) (0)1865 613340<u class=""></u><u class=""></u></span></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""><span style="font-size:9pt" class="">Lab manager: Dr Darragh Ennis<span class="m_1718352761905303641Apple-converted-space"> </span></span></span><a href="mailto:darragh.ennis@bioch.ox.ac.uk" style="color:purple;text-decoration:underline" target="_blank" class=""><span class=""><span style="font-size:9pt" class="">darragh.ennis@bioch.ox.<wbr class="">ac.uk</span></span><span class=""></span></a><span class=""><span style="font-size:9pt" class=""><span class="m_1718352761905303641Apple-converted-space"> </span>(44)
(0)1865 613271 / 613272 <u class=""></u><u class=""></u></span></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""><span style="font-size:9pt" class="">PA: </span></span><a href="mailto:jolanta.parkinson@bioch.ox.ac.uk" style="color:purple;text-decoration:underline" target="_blank" class=""><span class=""><span style="font-size:9pt" class="">jolanta.parkinson@bioch.ox.<wbr class="">ac.uk</span></span><span class=""></span></a><span class=""><span style="font-size:9pt" class=""> (44)
(0)1865 613218 </span></span><span class=""><span style="font-size:13.5pt" class=""><u class=""></u><u class=""></u></span></span></div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""><span style="font-size:9pt" class="">______________________________<wbr class="">______________________________<wbr class="">________________<u class=""></u><u class=""></u></span></span></div>
</div>
</div>
<div class="">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""><span style="font-size:9pt" class=""> </span></span></div>
</div>
</div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""><span style="font-size:9pt" class=""> </span></span></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
<div style="margin:0cm 0cm 12pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span><br class="m_1718352761905303641webkit-block-placeholder">
</div>
</div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></div>
</div>
</div>
</div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class="">______________________________<wbr class="">_________________<br class="">
ome-devel mailing list<br class="">
</span><a href="mailto:ome-devel@lists.openmicroscopy.org.uk" style="color:purple;text-decoration:underline" target="_blank" class=""><span class="">ome-devel@lists.<wbr class="">openmicroscopy.org.uk</span><span class=""></span></a><span class=""><br class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" target="_blank" class="">http://lists.openmicroscopy.<wbr class="">org.uk/mailman/listinfo/ome-<wbr class="">devel</a><u class=""></u><u class=""></u></span></div>
</div>
</blockquote>
</div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<span class=""> </span></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" 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;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;float:none;display:inline!important" class=""> </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;float:none;display:inline!important" class="">_____________________<wbr class="">__________________________</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" 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;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" 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;float:none;display:inline!important" class=""><a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank" class="">ome-devel@lists.<wbr class="">openmicroscopy.org.uk</a></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" 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;float:none;display:inline!important" class=""><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" target="_blank" class="">http://lists.openmicroscopy.<wbr class="">org.uk/mailman/listinfo/ome-<wbr class="">devel</a></span></div>
</blockquote>
</div>
<br class="">
</div>
</div>
______________________________<wbr class="">_________________<br class="">
ome-devel mailing list<br class="">
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank" class="">ome-devel@lists.<wbr class="">openmicroscopy.org.uk</a><br class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" target="_blank" class="">http://lists.openmicroscopy.<wbr class="">org.uk/mailman/listinfo/ome-<wbr class="">devel</a><br class="">
</div>
</blockquote>
</div>
<br class="">
<br class="">
<span style="font-size:10pt" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</div>
______________________________<wbr class="">_________________<br class="">
ome-devel mailing list<br class="">
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank" class="">ome-devel@lists.<wbr class="">openmicroscopy.org.uk</a><br class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" target="_blank" class="">http://lists.openmicroscopy.<wbr class="">org.uk/mailman/listinfo/ome-<wbr class="">devel</a><br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
<br class="">
<span style="font-size:10pt" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</div>
</div>
</div>
<br class="">
______________________________<wbr class="">_________________<br class="">
ome-devel mailing list<br class="">
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.<wbr class="">openmicroscopy.org.uk</a><br class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" rel="noreferrer" target="_blank" class="">http://lists.openmicroscopy.<wbr class="">org.uk/mailman/listinfo/ome-<wbr class="">devel</a><br class="">
<br class="">
</blockquote>
</div>
<br class="">
</div>
</div>
_______________________________________________<br class="">
ome-devel mailing list<br class="">
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.openmicroscopy.org.uk</a><br class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
<br class="">
<span style="font-size:10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</div>
_______________________________________________<br class="">ome-devel mailing list<br class=""><a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.openmicroscopy.org.uk</a><br class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel<br class=""></div></blockquote></div><br class=""></div></body></html>