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<p style="margin-top:0;margin-bottom:0">Hi Ilan</p>
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<p style="margin-top:0;margin-bottom:0">Thanks for your comments. Lots to think about, as always.</p>
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<p style="margin-top:0;margin-bottom:0">Regarding the workflow your lab is using-- it would be great if you or someone from the lab would share it here, or maybe even on the OME blog. If by workflow you mean a real script, is it anywhere at
<a href="https://github.com/MicronOxford" class="OWAAutoLink" id="LPlnk820134" previewremoved="true">
https://github.com/MicronOxford</a>? Could it be? We've so far failed to get funding for OMERO.figure and cool use cases we haven't thought of would help. It would be great to see what you are doing, understand your workflow, and get ideas how we might improve
things-- the spirit and practice of open source, and so on...</p>
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<p style="margin-top:0;margin-bottom:0">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
<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!</p>
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<p style="margin-top:0;margin-bottom:0">There is nothing to stop a journal including a link to an OMERO resource (e.g.,
<a href="https://omero.lifesci.dundee.ac.uk/figure/file/364219" class="OWAAutoLink" id="LPlnk516260" previewremoved="true">
https://omero.lifesci.dundee.ac.uk/figure/file/364219</a>) in a paper. They just need to do it! Maybe help us convince the journals that this would be a useful idea to consider??</p>
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<p style="margin-top:0;margin-bottom:0">Integrating OMERO.figure into IDR? Interesting suggestion-- we should look at the workflow and presentation carefully. As is often the case, it's less about the technical capability and more about the ease and accessibility
of the tool and workflow. </p>
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<p style="margin-top:0;margin-bottom:0">Thanks again for your thoughts! Keep them coming!</p>
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<p style="margin-top:0;margin-bottom:0">Cheers,</p>
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<p style="margin-top:0;margin-bottom:0">Jason<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>From:</b> ome-devel <ome-devel-bounces@lists.openmicroscopy.org.uk> on behalf of Ilan Davis <ilandavis@mac.com><br>
<b>Sent:</b> 01 February 2018 07:33:27<br>
<b>To:</b> OME External Developer List; King Charles House; darragh.ennis@bioch.ox.ac.uk; Richard Parton; David Pinto<br>
<b>Subject:</b> Re: [ome-devel] Updates on Data Publication</font>
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<div>Hi Jason
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<div>This is great and thanks for the update. Also congrats on your very nice paper in open bio. </div>
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<div>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>
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<div>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>
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<div>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>
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<div>Thanks</div>
<div>Regards</div>
<div>Ilan</div>
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<div id="x_AppleMailSignature">Sent from my iPhone</div>
<div><br>
On 1 Feb 2018, at 01:46, Jason Swedlow (Staff) <<a href="mailto:j.r.swedlow@dundee.ac.uk">j.r.swedlow@dundee.ac.uk</a>> wrote:<br>
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<div class="x_WordSection1">
<p class="x_MsoNormal"><span style="font-size:11.0pt" lang="EN-US">Dear All </span>
</p>
<p class="x_MsoNormal"><span style="font-size:11.0pt" lang="EN-US"> </span></p>
<p class="x_MsoNormal"><span style="font-size:11.0pt" lang="EN-US">Just a quick update on our recent activities in data publication.</span></p>
<p class="x_MsoNormal"><span style="font-size:11.0pt" lang="EN-US"> </span></p>
<p class="x_MsoNormal"><span style="font-size:11.0pt" lang="EN-US">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 <a href="https://idr.openmicroscopy.org/about/submission.html">https://idr.openmicroscopy.org/about/submission.html</a>.
</span></p>
<p class="x_MsoNormal"><span style="font-size:11.0pt" lang="EN-US"> </span></p>
<p class="x_MsoNormal"><span style="font-size:11.0pt" lang="EN-US">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">http://doi.org/<span style="" lang="EN-GB">10.1098/rsob.170099</span></a></span><span style="font-size:11.0pt" lang="EN-US">,</span><span style="font-size:11.0pt" lang="EN-US"> and the original image data is at
</span><span style="font-size:11.0pt"><a href="http://dx.doi.org/10.17867/10000109">http://dx.doi.org/10.17867/10000109</a></span><span style="font-size:11.0pt" lang="EN-US">. For more info, see our recent entry on the OME Blog (<a href="http://blog.openmicroscopy.org/community/2018/01/25/fair/">http://blog.openmicroscopy.org/community/2018/01/25/fair/</a>).
</span><span style="font-size:11.0pt"></span></p>
<p class="x_MsoNormal"><span style="font-size:11.0pt" lang="EN-US"> </span></p>
<p class="x_MsoNormal"><span style="font-size:11.0pt" lang="EN-US">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 <a href="https://arxiv.org/abs/1801.10189">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></p>
<p class="x_MsoNormal"><span style="font-size:11.0pt" lang="EN-US"> </span></p>
<p class="x_MsoNormal"><span style="font-size:11.0pt" lang="EN-US">As always, we welcome your thoughts, comments, critiques, and ideas.</span></p>
<p class="x_MsoNormal"><span style="font-size:11.0pt" lang="EN-US"> </span></p>
<p class="x_MsoNormal"><span style="font-size:11.0pt" lang="EN-US">Cheers,</span></p>
<p class="x_MsoNormal"><span style="font-size:11.0pt" lang="EN-US"> </span></p>
<p class="x_MsoNormal"><span style="font-size:11.0pt" lang="EN-US">Jason</span></p>
<p class="x_MsoNormal"><span style="font-size:11.0pt" lang="EN-US"> </span></p>
<p class="x_MsoNormal"><span style="font-size:11.0pt" lang="EN-US"> </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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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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