<div dir="ltr">I will definitely have a look - but it will take me a week or 2 - grant applications are getting in the way! <br></div><br><div class="gmail_quote"><div dir="ltr">On Fri, 28 Aug 2015 at 11:12 Munro, Ian <<a href="mailto:i.munro@imperial.ac.uk">i.munro@imperial.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div>Hi Seamus</div>
<div><br>
</div>
<div>As I’m currently at an impasse with ThunderSTORM I have added some code to PALM-siever to select and load a file annotation from OMERO</div>
<div>as an example.</div>
<div>Currently this is in my fork at <a href="https://github.com/imunro/palm-siever" target="_blank">https://github.com/imunro/palm-siever</a> but I’m happy to raise a PR if you want to pursue this?</div>
<div><br>
</div>
<div>The next step would be to add code to handle Simon’s OMERO table.</div>
<div>For it to work you also need to download the OMERO matlab plugin code from <a href="http://downloads.openmicroscopy.org/omero/5.1.3/" target="_blank">http://downloads.openmicroscopy.org/omero/5.1.3/</a>.</div>
<div>Just drop the contents into the OMERO.matlab directory that I’ve added.</div>
<div><br>
</div>
<div>All the best</div></div><div style="word-wrap:break-word">
<div><br>
</div>
<div>Ian</div></div><div style="word-wrap:break-word">
<div><br>
</div>
<div><br>
</div>
<br>
<div>
<div>On 26 Aug 2015, at 17:26, Simon Li <<a href="mailto:spli@dundee.ac.uk" target="_blank">spli@dundee.ac.uk</a>> wrote:</div>
<br>
<blockquote type="cite">
<div>
<div dir="ltr">
<div>Hi Ian, Seamus.<br>
<br>
That'd be great. I'm away for two weeks from Friday, but I'm happy to help if you get stuck.<br>
<br>
</div>
Simon<br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 26 August 2015 at 15:21, Munro, Ian <span dir="ltr"><<a href="mailto:i.munro@imperial.ac.uk" target="_blank">i.munro@imperial.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Seamus
<div><br>
</div>
<div>If you want to try this there is quite a bit of code for interfacing matlab applications to OMERO in </div>
<div><a href="https://github.com/openmicroscopy/Imperial-FLIMfit/tree/OME51" target="_blank">https://github.com/openmicroscopy/Imperial-FLIMfit/tree/OME51</a>.</div>
<div><br>
</div>
<div>Best Wishes</div>
<span><font color="#888888">
<div><br>
</div>
<div>Ian</div>
</font></span>
<div>
<div>
<div><br>
<div>
<div>On 26 Aug 2015, at 14:58, Seamus Holden <<a href="mailto:seamus.holden@gmail.com" target="_blank">seamus.holden@gmail.com</a>> wrote:</div>
<br>
<blockquote type="cite">
<div dir="ltr">
<div>
<div>For what it's worth, I'm happy to add this capability to PALMsiever too - not much work.<br>
<br>
</div>
Best <br>
</div>
Seamus<br>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Tue, 25 Aug 2015 at 14:03 Munro, Ian <<a href="mailto:i.munro@imperial.ac.uk" target="_blank">i.munro@imperial.ac.uk</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Seamus
<div><br>
</div>
<div>Not at all I’m happy to get any feedback I’m very much feeling my way here.</div>
<div>In the light of your comments and after discussion with the OME team we have moved on to Plan B. (or possibly E) which is to add to ThunderSTORM</div>
<div>the capability to load localisations from the data that Simon Li has generated.</div>
<div><br>
</div>
<div>Best Wishes </div>
</div>
<div style="word-wrap:break-word">
<div><br>
</div>
<div>Ian</div>
</div>
<div style="word-wrap:break-word">
<div><br>
</div>
<div>
<div>On 24 Aug 2015, at 11:38, Seamus Holden <<a href="mailto:seamus.holden@gmail.com" target="_blank">seamus.holden@gmail.com</a>> wrote:</div>
<br>
<blockquote type="cite">
<div dir="ltr">
<div>Hi Ian<br>
<br>
</div>
I should stress that although these comments are a bit negative I mean them only in a constructive fashion, and I am completely happy to be contradicted!<br>
<div><br>
<div>There are already a couple of rendering tools available - mainly PALMsiever (which I helped develop, open source), ThunderSTORM (open-source) and VisP (closed source). Being academic software, all of them are a bit buggy, and slowly updated, but essentially,
the rendering bit is a (largely) solved problem, software wise. And regards the bugs/ missing features - I would suggest rather than develop new software, just ask for commit rights on PALMsiever or ThunderSTORM - they are both on GitHub!<br>
<br>
The common localization format is on the other hand still an unsolved problem.The nicest point to my mind about focussing just on this aspect is that it's a small(-ish), well defined problem, which it would be quite useful to solve.
<br>
</div>
<div></div>
<div><br>
<div>Best wishes<br>
</div>
Seamus<br>
<p class="MsoNormal"><a name="msg-f:1510742935225437646_14f6a636e6341706_msg-f:1510481925494119892__MailAutoSig"><span style="color:#1f497d">Dr Seamus Holden</span></a></p>
<p class="MsoNormal"><span><span style="color:#1f497d">University Research Fellow</span></span></p>
<div><span><span style="color:#1f497d"> </span></span><br>
</div>
<p class="MsoNormal"><span><span style="color:#1f497d">Centre for Bacterial Cell Biology</span></span></p>
<p class="MsoNormal"><span><span style="color:#1f497d">Baddiley-Clark Building</span></span></p>
<p class="MsoNormal"><span><span style="color:#1f497d">Newcastle University</span></span></p>
<p class="MsoNormal"><span><span style="color:#1f497d">Richardson Road</span></span></p>
<p class="MsoNormal"><span><span style="color:#1f497d">Newcastle upon Tyne</span></span></p>
<p class="MsoNormal"><span><span style="color:#1f497d">NE2 4AX, United Kingdom</span></span></p>
<div><span><span style="color:#1f497d"> </span></span><br>
</div>
<p class="MsoNormal"><span><span style="color:#1f497d">Phone: <a href="tel:%2B44%20%280%29191%20208%203230" value="+441912083230" target="_blank">
+44 (0)191 208 3230</a></span></span></p>
<br>
</div>
<div><br>
<div class="gmail_quote">
<div dir="ltr">On Mon, 24 Aug 2015 at 10:09 Munro, Ian <<a href="mailto:i.munro@imperial.ac.uk" target="_blank">i.munro@imperial.ac.uk</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello All<br>
<br>
Does anyone have any comments on Kwasi’s document?.<br>
Based on his thoughts I’ve started looking at developing an open-source OMERO-capable<br>
reconstruction/rendering tool, although not full-time I fear, so progress is slow.<br>
<br>
If anyone has any thoughts it would be good to hear them at this early stage.<br>
<br>
Thanks<br>
<br>
Ian Munro<br>
<br>
Photonics Department<br>
Imperial College, London.<br>
<br>
On 7 Aug 2015, at 13:43, Kwasi Amoako Kwakwa <<a href="mailto:k.kwakwa@imperial.ac.uk" target="_blank">k.kwakwa@imperial.ac.uk</a>> wrote:<br>
<br>
> Hello All,<br>
><br>
> I am a postdoc in Paul French's group at Imperial working on<br>
> STORM/localization microscopy. I've been talking to Ian Munro a lot trying to<br>
> hash out what I think are the outstanding problems with storing and viewing<br>
> localization data and I thought it might be a good idea to share what I have<br>
> so far and see if people agree and if you have any suggestions or things to<br>
> add.<br>
><br>
> Thanks,<br>
> Kwasi Kwakwa<br>
><br>
><br>
> --<br>
> Kwasi A. Kwakwa<br>
> Research Associate, Photonics Department<br>
> Imperial College London<Localization Microscopy Issues.docx>_______________________________________________<br>
> ome-devel mailing list<br>
> <a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.openmicroscopy.org.uk</a><br>
> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" rel="noreferrer" target="_blank">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br>
<br>
_______________________________________________<br>
ome-devel mailing list<br>
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" rel="noreferrer" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br>
</blockquote>
</div>
</div>
</div>
</div>
_______________________________________________<br>
ome-devel mailing list<br>
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br>
</blockquote>
</div>
<br>
</div>
_______________________________________________<br>
ome-devel mailing list<br>
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" rel="noreferrer" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br>
</blockquote>
</div>
_______________________________________________<br>
ome-devel mailing list<br>
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</div>
<br>
_______________________________________________<br>
ome-devel mailing list<br>
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" rel="noreferrer" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br>
<br>
</blockquote>
</div>
<br>
</div>
<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</div>
_______________________________________________<br>
ome-devel mailing list<br>
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br>
</blockquote>
</div>
<br>
</div>
_______________________________________________<br>
ome-devel mailing list<br>
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" rel="noreferrer" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br>
</blockquote></div>