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<p class="MsoNormal"><span class="EmailStyle19">Hi Ilan<o:p></o:p></span></p>
<p class="MsoNormal"><span class="EmailStyle19"><o:p> </o:p></span></p>
<p class="MsoNormal"><span class="EmailStyle19">My €$£0.02.<o:p></o:p></span></p>
<p class="MsoNormal"><span class="EmailStyle19"><o:p> </o:p></span></p>
<p class="MsoNormal"><span class="EmailStyle19">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). <o:p></o:p></span></p>
<p class="MsoNormal"><span class="EmailStyle19"><o:p> </o:p></span></p>
<p class="MsoNormal"><span class="EmailStyle19">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!!!<o:p></o:p></span></p>
<p class="MsoNormal"><span class="EmailStyle19"><o:p> </o:p></span></p>
<p class="MsoNormal"><span class="EmailStyle19">We’ll discuss at the upcoming Users meeting, take in more feedback, and come up with a plan for taking these forward.<o:p></o:p></span></p>
<p class="MsoNormal"><span class="EmailStyle19"><o:p> </o:p></span></p>
<p class="MsoNormal"><span class="EmailStyle19">Huge thanks again.<o:p></o:p></span></p>
<p class="MsoNormal"><span class="EmailStyle19"><o:p> </o:p></span></p>
<p class="MsoNormal"><span class="EmailStyle19">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span class="EmailStyle19"><o:p> </o:p></span></p>
<p class="MsoNormal"><span class="EmailStyle19">Jason<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">William Moore <W.Moore@dundee.ac.uk><br>
<b>Date: </b>Tuesday, 22 May 2018 at 15:41<br>
<b>To: </b>OME Development <ome-devel@lists.openmicroscopy.org.uk><br>
<b>Cc: </b>Jason Swedlow <j.r.swedlow@dundee.ac.uk>, Joshua Titlow <joshua.titlow@bioch.ox.ac.uk>, mkaythomp_gmail_com <mkaythomp@gmail.com>, Darragh Ennis <darragh.ennis@bioch.ox.ac.uk>, Richard Parton <richard.parton@bioch.ox.ac.uk>, David Susano Pinto <david.pinto@bioch.ox.ac.uk><br>
<b>Subject: </b>Re: [ome-devel] Request for feature development for FIGURE - for discussion by the community<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><a name="_MailOriginalBody">Hi Illan, <o:p></o:p></a></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"> Thanks for the all the feedback.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">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.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">I’ll respond to the various requests below in-line...<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">On 16 May 2018, at 16:30, Ilan Davis <</span><a href="mailto:ilan.davis@bioch.ox.ac.uk"><span style="mso-bookmark:_MailOriginalBody">ilan.davis@bioch.ox.ac.uk</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody">>
wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Dear OME developer community
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">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…<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><b>Motivation</b></span><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Figure was developed to make it possible to make figures for papers directly from OMERO and bypassing illustrator and the like. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">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. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">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. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><b>Development requests</b></span><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">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. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">We have an existing feature request for “Stand-alone labels” (labels that can be placed anywhere on the page)
</span><a href="https://trello.com/c/wtu7IVuN/10-stand-alone-labels"><span style="mso-bookmark:_MailOriginalBody">https://trello.com/c/wtu7IVuN/10-stand-alone-labels</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody">. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Does this cover your needs or are there other improvements to the existing panel labels that you’d like to see?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">You can set font-sizes on labels already. Does “scalable text” include some other functionality or more flexible sizes?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">2) Create a hierarchy of folders housing figures so that figures can be organised in a sensible way over time, at scale. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><br>
The folders feature request is listed at </span><a href="https://trello.com/c/LwAVYUjm/165-save-figures-in-folders"><span style="mso-bookmark:_MailOriginalBody">https://trello.com/c/LwAVYUjm/165-save-figures-in-folders</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"> with
some discussion as to options and timescale<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">(which is currently limited by the OMERO model for Folders - so this needs to change first in OMERO).<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">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. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">A tagging system would consist of 2 main features.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">- ‘Add Tags’ dialog/panel - similar to that in webclient, and/or extend Auto-Tag (if users have lots of tokens in their figure names).<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">- Browse Tag hierarchy from within the figure app.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">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?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">NB: currently webclient (or Tag-searcher) will not display Tagged File-Annotations (figures).<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Card created at </span><a href="https://trello.com/c/X2lvut2c/192-add-tags-to-figures-browse-by-tag"><span style="mso-bookmark:_MailOriginalBody">https://trello.com/c/X2lvut2c/192-add-tags-to-figures-browse-by-tag</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">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. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Batch export of Figures was previously being discussed at
</span><a href="https://github.com/ome/omero-figure/issues/151"><span style="mso-bookmark:_MailOriginalBody">https://github.com/ome/omero-figure/issues/151</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"> (Josh
Titlow).<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">However, one of the main issues has been identified by David Pinto
</span><a href="https://github.com/ome/omero-figure/issues/289"><span style="mso-bookmark:_MailOriginalBody">https://github.com/ome/omero-figure/issues/289</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"> which
is the fact that the export creates a File Annotation on OMERO.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">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><a href="https://github.com/ome/omero-figure/pull/240"><span style="mso-bookmark:_MailOriginalBody">https://github.com/ome/omero-figure/pull/240</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"> 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.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">5) Allow more format of figure export especially .png<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">PNG export should be quite straightforward to implement. Created card at
</span><a href="https://trello.com/c/N0PQjMKJ/189-export-as-png"><span style="mso-bookmark:_MailOriginalBody">https://trello.com/c/N0PQjMKJ/189-export-as-png</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">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). <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">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<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">the workflow a bit and we’d probably want to make it optional in that case.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">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. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">This gives you the most flexibility and can be updated according to your needs without the UI and workflow changes for other users.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"> Thanks again for your input.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"> I look forward to more discussions at the OME meeting next week,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"> Regards,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"> Will.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">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"><span style="mso-bookmark:_MailOriginalBody">http://www.openmicroscopy.org/2018/05/22/figure-4-0-0.html</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">I welcome comments, clarifications, questions or counterpoints. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">with best regards<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Ilan<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><b>For transparency:</b></span><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><b>I am on the SAB of Zegami and on the SAB of OMERO-IDR</b></span><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">p.s.If you would like to know more about Zegami, please look up. </span><a href="https://zegami.com/"><span style="mso-bookmark:_MailOriginalBody">https://zegami.com/</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><b><span style="font-size:9.0pt">Prof. Ilan Davis </span></b></span><a href="mailto:ilan.davis@bioch.ox.ac.uk"><span style="mso-bookmark:_MailOriginalBody"><b><span style="font-size:9.0pt">ilan.davis@bioch.ox.ac.uk</span></b></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><b><span style="font-size:9.0pt">
</span></b></span><a href="http://www.ilandavis.com/"><span style="mso-bookmark:_MailOriginalBody"><b><span style="font-size:9.0pt">http://www.ilandavis.com</span></b></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:9.0pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"></span><a href="https://twitter.com/ilandavis"><span style="mso-bookmark:_MailOriginalBody"><b><span style="font-size:9.0pt">https://twitter.com/ilandavis</span></b></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:13.5pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:9.0pt">Department of Biochemistry, The University of Oxford, South Parks Road, OXFORD OX1 3QU, UK<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:9.0pt">Direct Office No: (44) (0)1865 613265 Office Fax: (44) (0)1865 613340<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:9.0pt">Lab manager: Dr Darragh Ennis
</span></span><a href="mailto:darragh.ennis@bioch.ox.ac.uk"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:9.0pt">darragh.ennis@bioch.ox.ac.uk</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:9.0pt">
(44) (0)1865 613271 / 613272 <o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:9.0pt">PA: </span></span><a href="mailto:jolanta.parkinson@bioch.ox.ac.uk"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:9.0pt">jolanta.parkinson@bioch.ox.ac.uk</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:9.0pt"> (44)
(0)1865 613218 </span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:13.5pt"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">_______________________________________________<br>
ome-devel mailing list<br>
</span><a href="mailto:ome-devel@lists.openmicroscopy.org.uk"><span style="mso-bookmark:_MailOriginalBody">ome-devel@lists.openmicroscopy.org.uk</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><br>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel<o:p></o:p></span></p>
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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