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<div>Hi Alan</div>
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<div>I had a brief chat today with Ian and we thought it will be good to maybe have a discussion later on this week.</div>
<div>Will Thursday at 2pm work you?</div>
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<div>Cheers</div>
<div>Jmarie</div>
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<span style="font-weight:bold">From: </span>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>
<span style="font-weight:bold">Reply-To: </span>OME External Developer List <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, 7 January 2016 14:20<br>
<span style="font-weight:bold">To: </span>OME External Developer List <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ome-devel] Spectral Chemical Imaging Data<br>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Hi Ian,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">I’ve started trying to read about 8D OME storage (<a href="https://www.openmicroscopy.org/site/support/ome-model/developers/6d-7d-and-8d-storage.html">https://www.openmicroscopy.org/site/support/ome-model/developers/6d-7d-and-8d-storage.html</a>
), but I think I need to become a little more familiar with OME to know which option will map best to our data.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">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.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">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 (<a href="http://www.peptideatlas.org/tmp/mzML1.1.0.html">http://www.peptideatlas.org/tmp/mzML1.1.0.html</a>
). Is there an equivalent of the Bio-Formats reader for metadata? How is metadata typically stored for other formats?
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Best wishes,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Alan<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;">From:</span></b><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;"> 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>Munro, Ian<br>
<b>Sent:</b> 07 January 2016 12:58<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"><o:p> </o:p></p>
<p class="MsoNormal">Hi Alan <o:p></o:p></p>
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<p class="MsoNormal">That would certainly be the best way to get things moving.<o:p></o:p></p>
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<p class="MsoNormal">There are two questions that need to be addressed first though.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">2) What to do about metadata? Which depends I suspect on your needs.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hopefully the core OMERO may have some input here.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best Wishes <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Ian <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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></p>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Hi Ian,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">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><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">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><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Best wishes,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Alan</span><o:p></o:p></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;"> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;">ome-devel
[<a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk"><span style="color:purple">mailto:ome-devel-bounces@lists.openmicroscopy.org.uk</span></a>]<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 <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk"><span style="color:purple">ome-devel@lists.openmicroscopy.org.uk</span></a>><br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [ome-devel] Spectral Chemical Imaging Data</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hi Alan <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Sorry I should have said that you need to select user Ian Munro when you select the group.<o:p></o:p></p>
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<p class="MsoNormal">By default the OMERO clients show you your own data only.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Ian <image001.png><o:p></o:p></p>
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<p class="MsoNormal">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></p>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Hi Ian,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">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><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"><image001.png></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">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><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">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><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Thanks again for all your time and effort,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Alan</span><o:p></o:p></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;"> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;">ome-devel
[<a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk"><span style="color:purple">mailto:ome-devel-bounces@lists.openmicroscopy.org.uk</span></a>]<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 <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk"><span style="color:purple">ome-devel@lists.openmicroscopy.org.uk</span></a>><br>
<b>Subject:</b><span class="apple-converted-space"> </span>[ome-devel] Spectral Chemical Imaging Data</span><o:p></o:p></p>
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<p class="MsoNormal">Happy New Year to you as well Alan.<span class="apple-converted-space"> </span><o:p></o:p></p>
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<p class="MsoNormal">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></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">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></p>
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<p class="MsoNormal">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></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">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></p>
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<p class="MsoNormal">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></p>
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<p class="MsoNormal">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></p>
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<p class="MsoNormal">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></p>
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<p class="MsoNormal">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></p>
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<p class="MsoNormal">N.B. you will need to change the background from the default value of 200 to 0.<o:p></o:p></p>
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<p class="MsoNormal">The screenshot illustrates what I see when I do this.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">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></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I hope all that makes sense.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Best Regards<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Ian <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><image002.png><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size: 10pt; font-family: Helvetica, sans-serif;">_______________________________________________<br>
ome-devel mailing list<br>
</span><a href="mailto:ome-devel@lists.openmicroscopy.org.uk"><span style="font-size: 10pt; font-family: Helvetica, sans-serif; color: purple;">ome-devel@lists.openmicroscopy.org.uk</span></a><span style="font-size: 10pt; font-family: Helvetica, sans-serif;"><br>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size: 10pt; font-family: Helvetica, sans-serif;">_______________________________________________<br>
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