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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi Jean-Marie,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Monday 2pm works great for me.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Alan<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> ome-devel [mailto:ome-devel-bounces@lists.openmicroscopy.org.uk]
<b>On Behalf Of </b>Jean-Marie Burel (Staff)<br>
<b>Sent:</b> 12 January 2016 09:22<br>
<b>To:</b> OME External Developer List <ome-devel@lists.openmicroscopy.org.uk><br>
<b>Subject:</b> Re: [ome-devel] Spectral Chemical Imaging Data<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"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">Hi Alan<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">Monday will work<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">Will Monday 2pm UK be a suitable time for you?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">Cheers<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">Jmarie<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">From:
</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">ome-devel <<a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk">ome-devel-bounces@lists.openmicroscopy.org.uk</a>> on behalf of Alan Race <<a href="mailto:alan.race@npl.co.uk">alan.race@npl.co.uk</a>><br>
<b>Reply-To: </b>OME External Developer List <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>><br>
<b>Date: </b>Monday, 11 January 2016 17:25<br>
<b>To: </b>OME External Developer List <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>><br>
<b>Subject: </b>Re: [ome-devel] Spectral Chemical Imaging Data<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Jean-Marie,</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">That sounds good. Unfortunately I will be out of the office on Thursday and am busy for most of Friday, perhaps next Monday might work?</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks,</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Alan</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> ome-devel [<a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk">mailto:ome-devel-bounces@lists.openmicroscopy.org.uk</a>]
<b>On Behalf Of </b>Jean-Marie Burel (Staff)<br>
<b>Sent:</b> 11 January 2016 14:42<br>
<b>To:</b> OME External Developer List <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>><br>
<b>Subject:</b> Re: [ome-devel] Spectral Chemical Imaging Data</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">Hi Alan</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">I had a brief chat today with Ian and we thought it will be good to maybe have a discussion later on this week.</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">Will Thursday at 2pm work you?</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">Cheers</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">Jmarie</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">From:
</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">ome-devel <</span><span style="color:black"><a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">ome-devel-bounces@lists.openmicroscopy.org.uk</span></a></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">>
on behalf of Alan Race <</span><span style="color:black"><a href="mailto:alan.race@npl.co.uk"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">alan.race@npl.co.uk</span></a></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">><br>
<b>Reply-To: </b>OME External Developer List <</span><span style="color:black"><a href="mailto:ome-devel@lists.openmicroscopy.org.uk"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">ome-devel@lists.openmicroscopy.org.uk</span></a></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">><br>
<b>Date: </b>Thursday, 7 January 2016 14:20<br>
<b>To: </b>OME External Developer List <</span><span style="color:black"><a href="mailto:ome-devel@lists.openmicroscopy.org.uk"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">ome-devel@lists.openmicroscopy.org.uk</span></a></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">><br>
<b>Subject: </b>Re: [ome-devel] Spectral Chemical Imaging Data</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Ian,</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I’ve started trying to read about 8D OME storage (</span><span style="color:black"><a href="https://www.openmicroscopy.org/site/support/ome-model/developers/6d-7d-and-8d-storage.html"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">https://www.openmicroscopy.org/site/support/ome-model/developers/6d-7d-and-8d-storage.html</span></a></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">
), but I think I need to become a little more familiar with OME to know which option will map best to our data.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I can certainly help shed some light on number 2 though. A lot of the metadata included within the file is to do with how the data should be read in, parsed,
processed etc. and can be handled by my library/the bio-formats reader and isn’t necessary for the end user to see.
</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">The remaining metadata helps to describe the experiment (ideally in sufficient detail that it could be repeated) and it would be useful to be able to view/query
this, but that isn’t necessarily a priority. All of the metadata can be boiled down to (tag, value) pairs, where there are very few *<b>required</b>* tags, and the majority are optional descriptors organised in a hierarchy (</span><span style="color:black"><a href="http://www.peptideatlas.org/tmp/mzML1.1.0.html"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">http://www.peptideatlas.org/tmp/mzML1.1.0.html</span></a></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">
). Is there an equivalent of the Bio-Formats reader for metadata? How is metadata typically stored for other formats?
</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Best wishes,</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Alan</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> ome-devel [</span><span style="color:black"><a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">mailto:ome-devel-bounces@lists.openmicroscopy.org.uk</span></a></span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">]
<b>On Behalf Of </b>Munro, Ian<br>
<b>Sent:</b> 07 January 2016 12:58<br>
<b>To:</b> OME External Developer List <</span><span style="color:black"><a href="mailto:ome-devel@lists.openmicroscopy.org.uk"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">ome-devel@lists.openmicroscopy.org.uk</span></a></span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">><br>
<b>Subject:</b> Re: [ome-devel] Spectral Chemical Imaging Data</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Hi Alan <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">That would certainly be the best way to get things moving.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">There are two questions that need to be addressed first though.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">1) How best to fit this data into the 8D OMERO model ? I tried 2 options, as examples, but there are many other possibilities.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">2) What to do about metadata? Which depends I suspect on your needs.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Hopefully the core OMERO may have some input here.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Best Wishes <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Ian <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">On 7 Jan 2016, at 12:36, Alan Race <<a href="mailto:alan.race@npl.co.uk">alan.race@npl.co.uk</a>> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Ian,</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Okay great, thanks, that worked and I can download the data and open in FLIMfit. This style of viewing/processing with our current tools but with the OMERO backend
would actually be great.<span class="apple-converted-space"> </span></span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I’m not sure if you saw my additional questions below the image in the previous email, but as for the next step, what do you think would be the best way to proceed?
I suspect that probably it would be for me to write a Bio-Formats reader for imzML?</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Best wishes,</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Alan</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> </span></span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">ome-devel
[</span><span style="color:black"><a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:purple">mailto:ome-devel-bounces@lists.openmicroscopy.org.uk</span></a></span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">]<span class="apple-converted-space"> </span><b>On
Behalf Of<span class="apple-converted-space"> </span></b>Munro, Ian<br>
<b>Sent:</b><span class="apple-converted-space"> </span>07 January 2016 12:16<br>
<b>To:</b><span class="apple-converted-space"> </span>OME External Developer List <</span><span style="color:black"><a href="mailto:ome-devel@lists.openmicroscopy.org.uk"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:purple">ome-devel@lists.openmicroscopy.org.uk</span></a></span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">><br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [ome-devel] Spectral Chemical Imaging Data</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Hi Alan <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Sorry I should have said that you need to select user Ian Munro when you select the group.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">By default the OMERO clients show you your own data only.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Ian <image001.png><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">On 7 Jan 2016, at 12:06, Alan Race <<a href="mailto:alan.race@npl.co.uk"><span style="color:purple">alan.race@npl.co.uk</span></a>> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Ian,</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I have logged in and can select the “Experimental Formats” group, but I still don’t see any data. I could be looking in the wrong place I guess?</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><image001.png></span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hopefully it shouldn’t be too difficult a task for me to implement a Bio-Formats reader as I’ve already written a library to read imzML data, so theoretically
should be able to just call the appropriate methods in that. How would be the best way to go about writing a Bio-Formats reader? Can anyone contribute to the Bio-Formats project?</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thank you very much for the details and the illustration of the data in FLIMfit. The image looks correct, but the spectral dimension looks wrong – is that due
to FLIMfit somehow, or should that be displaying the full raw spectral dimension? From your experience, how difficult was it to adapt your tools to be OMERO clients?</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks again for all your time and effort,</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Alan</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> </span></span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">ome-devel
[</span><span style="color:black"><a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:purple">mailto:ome-devel-bounces@lists.openmicroscopy.org.uk</span></a></span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">]<span class="apple-converted-space"> </span><b>On
Behalf Of<span class="apple-converted-space"> </span></b>Munro, Ian<br>
<b>Sent:</b><span class="apple-converted-space"> </span>07 January 2016 09:56<br>
<b>To:</b><span class="apple-converted-space"> </span>OME External Developer List <</span><span style="color:black"><a href="mailto:ome-devel@lists.openmicroscopy.org.uk"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:purple">ome-devel@lists.openmicroscopy.org.uk</span></a></span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">><br>
<b>Subject:</b><span class="apple-converted-space"> </span>[ome-devel] Spectral Chemical Imaging Data</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Happy New Year to you as well Alan.<span class="apple-converted-space"> </span><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">If you log in again now and change group to “Experimental Formats” you should hopefully be able to see some data under “Mass spec proof of concept/MouseCerebellum”.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">If this file format were to be supported in OME the first step would be to write a Bio-Formats reader. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">In order to give a flavour of what that might look like I have attempted to extract the data (N.B. not metadata) from your file and write it into OME-TIFF files for which a reader already exists.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">The first file there “MouseCerebellumC" - I have mapped your data into the 5D OME data model with m/z as channels , which seemed to me most appropriate.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Unfortunately this image is not easy to view using the standard OMERO clients which, for historical reasons, interpret large numbers of channels as time. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">From our earlier discussions, however it seemed likely that you would want a spectrum oriented view so in the second file “MouseCerebellumT” I’ve stored the data as if it were FLIM data with m/z mapped to time(t).<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">This will allow you examine the data using the FLIMfit tool <a href="http://downloads.openmicroscopy.org/flimfit/4.9.1/"><span style="color:purple">http://downloads.openmicroscopy.org/flimfit/4.9.1/</span></a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Frustratingly, you cannot, I’m afraid, log on to the demo server directly from FLIMfit as a version compatible with OMERO 5.2 has not yet been released so it will be necessary to download the file as described
in <a href="http://help.openmicroscopy.org/export.html#download"><span style="color:purple">http://help.openmicroscopy.org/export.html#download</span></a> and open locally.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">N.B. you will need to change the background from the default value of 200 to 0.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">The screenshot illustrates what I see when I do this.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Obviously I’m not suggesting that FLIMfit is appropriate for your data, but attempting to illustrate how it might look if you were to adapt your existing tools to be OMERO clients.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">I hope all that makes sense.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Best Regards<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Ian <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:black">_______________________________________________<br>
ome-devel mailing list<br>
</span><span style="color:black"><a href="mailto:ome-devel@lists.openmicroscopy.org.uk"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:purple">ome-devel@lists.openmicroscopy.org.uk</span></a></span><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:black"><br>
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</span><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:black">The University of Dundee is a registered Scottish Charity, No: SC015096</span><span style="color:black"><o:p></o:p></span></p>
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