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Hi Ilan,
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<div class=""> Thanks for all the details.</div>
<div class="">I’ve added notes to various cards and I think our understanding of most of these features is getting pretty clear now.</div>
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<div class="">Certainly seeing your workflow and discussing next week with Josh and MK will be a big help - I look forward to that.</div>
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<div class="">To summarise, this is the list of cards that I’ve created / added comments to and can form the basis of further discussions.</div>
<div class=""><a href="https://trello.com/c/wtu7IVuN/10-stand-alone-labels" class="">https://trello.com/c/wtu7IVuN/10-stand-alone-labels</a></div>
<div class=""><a href="https://trello.com/c/LwAVYUjm/165-save-figures-in-folders" class="">https://trello.com/c/LwAVYUjm/165-save-figures-in-folders</a></div>
<div class=""><a href="https://trello.com/c/X2lvut2c/192-add-tags-to-figures-browse-by-tag" class="">https://trello.com/c/X2lvut2c/192-add-tags-to-figures-browse-by-tag</a></div>
<div class=""><a href="https://trello.com/c/Ugw3YgLz/184-batch-export-figures" class="">https://trello.com/c/Ugw3YgLz/184-batch-export-figures</a></div>
<div class=""><a href="https://trello.com/c/N0PQjMKJ/189-export-as-png" class="">https://trello.com/c/N0PQjMKJ/189-export-as-png</a></div>
<div class=""><a href="https://trello.com/c/8vNGPi2n/190-export-without-scripting-service" class="">https://trello.com/c/8vNGPi2n/190-export-without-scripting-service</a></div>
<div class=""><a href="https://trello.com/c/rHv0db8f/193-export-with-metadata-tags" class="">https://trello.com/c/rHv0db8f/193-export-with-metadata-tags</a></div>
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<div class=""> Regards,</div>
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<div class=""> Will.</div>
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<div class="">On 22 May 2018, at 22:06, Ilan Davis <<a href="mailto:ilandavis@me.com" class="">ilandavis@me.com</a>> wrote:</div>
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Many thanks Will for focusing this discussion to be more specific. I think there are others in my team who can better answer a few points, I will put their names in red in the hope that they will see this and contribute. Apologies if I get wrong end of the
stick on any of these points.
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<div 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. </div>
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<div class="">We have an existing feature request for “Stand-alone labels” (labels that can be placed anywhere on the page) <a href="https://trello.com/c/wtu7IVuN/10-stand-alone-labels" class="">https://trello.com/c/wtu7IVuN/10-stand-alone-labels</a>. </div>
<div class="">Does this cover your needs or are there other improvements to the existing panel labels that you’d like to see?</div>
<div class="">You can set font-sizes on labels already. Does “scalable text” include some other functionality or more flexible sizes?</div>
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<div class=""><font color="#ff2600" class="">Josh and Darragh are better placed to answer this. I think the stand-alone labels is one issue and text that can be put anywhere inside a panel is another. I think I may have been wrong about the scalability issue
- I think it is scalable currently. </font></div>
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<div class="">2) Create a hierarchy of folders housing figures so that figures can be organised in a sensible way over time, at scale. </div>
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The folders feature request is listed at <a href="https://trello.com/c/LwAVYUjm/165-save-figures-in-folders" class="">https://trello.com/c/LwAVYUjm/165-save-figures-in-folders</a> with some discussion as to options and timescale</div>
<div class="">(which is currently limited by the OMERO model for Folders - so this needs to change first in OMERO).</div>
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<div class=""><font color="#ff2600" class="">If I understand you correctly, the file hierarchy would have to be limited in the same way the OMERO file hierarchy is limited (not like a file system).
<b class="">That would be fine, </b>as Figures correspond to groups of data on OMERO (sessions on the microscopes or data collections or whatever). </font></div>
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<div 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. </div>
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<div class="">A tagging system would consist of 2 main features.</div>
<div 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).</div>
<div class="">- Browse Tag hierarchy from within the figure app.</div>
<div 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?</div>
<div class="">NB: currently webclient (or Tag-searcher) will not display Tagged File-Annotations (figures).</div>
<div class="">Card created at <a href="https://trello.com/c/X2lvut2c/192-add-tags-to-figures-browse-by-tag" class="">https://trello.com/c/X2lvut2c/192-add-tags-to-figures-browse-by-tag</a> </div>
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<div class=""><font color="#ff2600" class="">This is getting a bit technical (I do not know how these things are built). But is it possible for the autotage programme to deal with each figure like an OMERO image and associate tags with it in the same way? </font></div>
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<div class=""><font color="#ff2600" class="">For our current way of operating we would want to export the list of figure names with list of associated tags in csv format. Name of tag on the top of the column and 1 or 0 indicating wether the tag applies to the
figure image. <b class="">Josh, MK?</b></font></div>
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<div 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. </div>
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<div class="">Batch export of Figures was previously being discussed at <a href="https://github.com/ome/omero-figure/issues/151" class="">https://github.com/ome/omero-figure/issues/151</a> (Josh Titlow).</div>
<div class="">However, one of the main issues has been identified by David Pinto <a href="https://github.com/ome/omero-figure/issues/289" class="">https://github.com/ome/omero-figure/issues/289</a> which is the fact that the export creates a File Annotation
on OMERO.</div>
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<div 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 <a href="https://github.com/ome/omero-figure/pull/240" class="">https://github.com/ome/omero-figure/pull/240</a> 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.</div>
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<div class=""><span style="color: rgb(255, 38, 0);" class="">I am not sure whether we are talking at cross purposes. At the moment you can export a figure with a pull down menu - but only one at a time. All I am asking for is to be able to pull down a menu,
see a long list of figures and select lots of them to export in batch. We have hundreds and hundreds of figures, so exporting one at a time is really impractical. Surelly this is not a big programming task. The creation of of file annotation - I do not understand
- as the export works fine at the moment as it is. </span></div>
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<div class="">5) Allow more format of figure export especially .png</div>
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PNG export should be quite straightforward to implement. Created card at <a href="https://trello.com/c/N0PQjMKJ/189-export-as-png" class="">https://trello.com/c/N0PQjMKJ/189-export-as-png</a> </div>
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<div class=""><font color="#ff2600" class="">Thanks - PNG is very useful as it works better in ppt and keynote than pdf (I see lots of weird stuff with resolution in conferences that is due to embedding pdf in keynote - mac / PC conversion etc. etc.). It also
happens to be the easy format of Zegami. </font></div>
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<div 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). </div>
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<div 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</div>
<div class="">the workflow a bit and we’d probably want to make it optional in that case.</div>
<div 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. </div>
<div class="">This gives you the most flexibility and can be updated according to your needs without the UI and workflow changes for other users.</div>
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<div class=""><font color="#ff2600" class="">In addition to exporting the tags in csv format files, it would be good to export the microscope metadata - or any metadata associated with the parent images in OMERO that are used to make figures. The hard part
is that I do not know how to export all the different metadata sensibly - i.e. from multiple different OMERO images to associate with one figure. Perhaps just be very expansive. Again a csv file with the first column being the same of the figure and the subsequent
columns listing all tags and metadata. But admittedly, that does not sound particularly sensible- probably needs a much cleverer approach for the microscope metadata. <b class="">MK. Josh?</b></font></div>
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<div class="">Thanks again for your thoughtful comments and time it took to understand all my points. Not that easy to explain them in writing. </div>
<div class="">Hopefully Josh and MK can explain some of the details of our workflow with examples much more easily. </div>
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<div class="">Regards</div>
<div class="">Ilan</div>
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<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>
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<div class="">On 22 May 2018, at 15:41, William Moore (Staff) <<a href="mailto:W.Moore@dundee.ac.uk" class="">W.Moore@dundee.ac.uk</a>> wrote:</div>
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Illan, </span>
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Thanks for the all the feedback.</div>
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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.</div>
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I’ll respond to the various requests below in-line...</div>
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<div class="">On 16 May 2018, at 16:30, Ilan Davis <<a href="mailto:ilan.davis@bioch.ox.ac.uk" class="">ilan.davis@bioch.ox.ac.uk</a>> wrote:</div>
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Dear OME developer community
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<div 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…<br class="">
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<div class=""><b class="">Motivation</b></div>
<div class="">Figure was developed to make it possible to make figures for papers directly from OMERO and bypassing illustrator and the like. </div>
<div 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. </div>
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<div 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. </div>
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<div class=""><b class="">Development requests</b></div>
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<div 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. </div>
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<div class="">We have an existing feature request for “Stand-alone labels” (labels that can be placed anywhere on the page)<span class="Apple-converted-space"> </span><a href="https://trello.com/c/wtu7IVuN/10-stand-alone-labels" class="">https://trello.com/c/wtu7IVuN/10-stand-alone-labels</a>. </div>
<div class="">Does this cover your needs or are there other improvements to the existing panel labels that you’d like to see?</div>
<div class="">You can set font-sizes on labels already. Does “scalable text” include some other functionality or more flexible sizes?</div>
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<div class="">2) Create a hierarchy of folders housing figures so that figures can be organised in a sensible way over time, at scale. </div>
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The folders feature request is listed at<span class="Apple-converted-space"> </span><a href="https://trello.com/c/LwAVYUjm/165-save-figures-in-folders" class="">https://trello.com/c/LwAVYUjm/165-save-figures-in-folders</a> with some discussion as to options
and timescale</div>
<div class="">(which is currently limited by the OMERO model for Folders - so this needs to change first in OMERO).</div>
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<div 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. </div>
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<div class="">A tagging system would consist of 2 main features.</div>
<div 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).</div>
<div class="">- Browse Tag hierarchy from within the figure app.</div>
<div 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?</div>
<div class="">NB: currently webclient (or Tag-searcher) will not display Tagged File-Annotations (figures).</div>
<div class="">Card created at <a href="https://trello.com/c/X2lvut2c/192-add-tags-to-figures-browse-by-tag" class="">https://trello.com/c/X2lvut2c/192-add-tags-to-figures-browse-by-tag</a> </div>
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<div 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. </div>
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<div class="">Batch export of Figures was previously being discussed at<span class="Apple-converted-space"> </span><a href="https://github.com/ome/omero-figure/issues/151" class="">https://github.com/ome/omero-figure/issues/151</a> (Josh Titlow).</div>
<div class="">However, one of the main issues has been identified by David Pinto<span class="Apple-converted-space"> </span><a href="https://github.com/ome/omero-figure/issues/289" class="">https://github.com/ome/omero-figure/issues/289</a> which is the fact
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<div 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="Apple-converted-space"> </span><a href="https://github.com/ome/omero-figure/pull/240" class="">https://github.com/ome/omero-figure/pull/240</a> 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.</div>
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<div class="">5) Allow more format of figure export especially .png</div>
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PNG export should be quite straightforward to implement. Created card at<span class="Apple-converted-space"> </span><a href="https://trello.com/c/N0PQjMKJ/189-export-as-png" class="">https://trello.com/c/N0PQjMKJ/189-export-as-png</a> </div>
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<div 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). </div>
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<div 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</div>
<div class="">the workflow a bit and we’d probably want to make it optional in that case.</div>
<div 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. </div>
<div class="">This gives you the most flexibility and can be updated according to your needs without the UI and workflow changes for other users.</div>
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<div class=""> Thanks again for your input.</div>
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<div class=""> I look forward to more discussions at the OME meeting next week,</div>
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<div class=""> Regards,</div>
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<div class=""> Will.</div>
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<div class="">PS. Another release of OMERO.figure just went out today: <a href="http://www.openmicroscopy.org/2018/05/22/figure-4-0-0.html" class="">http://www.openmicroscopy.org/2018/05/22/figure-4-0-0.html</a></div>
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<div class="">I welcome comments, clarifications, questions or counterpoints. </div>
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<div class="">with best regards</div>
<div class="">Ilan</div>
<div class=""><b class="">For transparency:</b></div>
<div class=""><b class="">I am on the SAB of Zegami and on the SAB of OMERO-IDR</b></div>
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<div class="">p.s.If you would like to know more about Zegami, please look up. <a href="https://zegami.com/" class="">https://zegami.com/</a></div>
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<div class="" style="font-size: 12px;">____________________________________________________________________________</div>
<div class="" style="font-size: 12px;"><b class="">Prof. Ilan Davis <a href="mailto:ilan.davis@bioch.ox.ac.uk" class="">ilan.davis@bioch.ox.ac.uk</a><span class="Apple-converted-space"> </span> <span class="Apple-converted-space"> </span><a href="http://www.ilandavis.com/" class="">http://www.ilandavis.com</a></b></div>
<div class=""><span class="" style="font-size: 12px;"><b class=""><a href="https://twitter.com/ilandavis" class="">https://twitter.com/ilandavis</a></b></span></div>
<div class="" style="font-size: 12px;">Department of Biochemistry, The University of Oxford, South Parks Road, OXFORD OX1 3QU, UK</div>
<div class="" style="font-size: 12px;">Direct Office No: (44) (0)1865 613265 Office Fax: (44) (0)1865 613340</div>
<div class="" style="font-size: 12px;">Lab manager: Dr Darragh Ennis<span class="Apple-converted-space"> </span><a href="mailto:darragh.ennis@bioch.ox.ac.uk" class="">darragh.ennis@bioch.ox.ac.uk</a><span class="Apple-converted-space"> </span>(44) (0)1865 613271
/ 613272 </div>
<div class=""><span class="" style="font-size: 12px;">PA: </span><span class="" style="text-align: -webkit-auto;"><span class="" style="font-size: 12px;"><a href="mailto:jolanta.parkinson@bioch.ox.ac.uk" class="">jolanta.parkinson@bioch.ox.ac.uk</a> (44)
(0)1865 </span></span><span class="" style="text-align: -webkit-auto; font-size: 12px;">613218</span><span class="" style="text-align: -webkit-auto; font-size: 12px;"> </span></div>
<div class="" style="font-size: 12px;">____________________________________________________________________________</div>
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