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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 Ian,<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">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?<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"><img width="1280" height="264" id="Picture_x0020_1" src="cid:image001.png@01D14942.A78908E0"></span><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"><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">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?
<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">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?<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 again for all your time and effort,<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>
<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>Munro, Ian<br>
<b>Sent:</b> 07 January 2016 09:56<br>
<b>To:</b> OME External Developer List <ome-devel@lists.openmicroscopy.org.uk><br>
<b>Subject:</b> [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">Happy New Year to you as well 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">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"><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/">http://downloads.openmicroscopy.org/flimfit/4.9.1/</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">http://help.openmicroscopy.org/export.html#download</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"><img border="0" width="1168" height="751" id="_x0032_549240E-D7C7-4CE7-BA82-B4BC16F8D7B6" src="cid:image002.png@01D14943.C6B237E0"><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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