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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 Josh,<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 for your email and the information on current progress. The number of channels in the data can certainly be a challenge.
The data that I shared was actually relatively low mass resolution data (Fourier Transform based instruments can produce spectra with an order of magnitude more channels). No worries about the delay though. If there is any way that I can help in this I would
be very happy to, feel free to get in touch.<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">Happy holidays,<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;mso-fareast-language:EN-US">Alan<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>Josh Moore<br>
<b>Sent:</b> 17 December 2015 15:56<br>
<b>To:</b> <ome-devel@lists.openmicroscopy.org.uk> <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">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">On Wed, Nov 18, 2015 at 3:41 PM, Alan Race <<a href="mailto:alan.race@npl.co.uk" target="_blank">alan.race@npl.co.uk</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">MSiReader uses the code that I wrote to parse imzML (there’s a JAR file included in there called imzMLConverter)
so it should work well with our data.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">The resolution in m/z doesn’t vary from pixel to pixel (potentially very slightly, but mass resolution
is primarily influenced by the instrument) however, only the non-zero intensities are stored and we may detect very different ions in any two pixels (hence very different spectra lengths). Thank you for your help and insight so far and also for your continued
efforts.</span><o:p></o:p></p>
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<p class="MsoNormal">Just a pre-holiday email to let you know that this hasn't dropped off our radar. Ian was working on extracting the data from your sample file and storing it first into an OME-TIFF with m/z as channels. This <span style="font-size:9.5pt">exposed
some limitations in the existing clients when handling data with such a large number of channels. And second with m/z along the time dimension and a FLIM style annotation to show what mass spec data might look like if a FLIMfit style client were written.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.5pt">A possible next step would be to make these available on a demo server to discuss possible next steps. Just with the release of OMERO 5.2.1 and the holidays, that won't be before January.</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"><span style="font-size:9.5pt">Hopefully you and yours enjoy the time (one way or the other) until then!</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.5pt">~Josh.</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" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Regards, </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Alan</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><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"> Munro,
Ian [mailto:</span><a href="mailto:i.munro@imperial.ac.uk" target="_blank"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">i.munro@imperial.ac.uk</span></a><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">]
<br>
<b>Sent:</b> 18 November 2015 14:33<br>
<b>To:</b> Alan Race <</span><a href="mailto:alan.race@npl.co.uk" target="_blank"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">alan.race@npl.co.uk</span></a><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">><br>
<b>Cc:</b> </span><a href="mailto:p.walczysko@dundee.ac.uk" target="_blank"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">p.walczysko@dundee.ac.uk</span></a><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">;
</span><a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">ome-devel@lists.openmicroscopy.org.uk</span></a><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><br>
<b>Subject:</b> Re: [ome-devel] Spectral Chemical Imaging Data</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thanks Alan
<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I’ve started experimenting using this software <a href="http://www4.ncsu.edu/~dcmuddim/msireader.html" target="_blank">http://www4.ncsu.edu/~dcmuddim/msireader.html</a> and what
I’m seeing <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">seems to correspond well with your description so I think I’m ok with software for now.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I take it then that the resolution in m/z varies as well from pixel to pixel? If so I may have underestimated the difficulty of storing your data into OMERO. I’ll take this back
to the core team for their thoughts.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Regards<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Ian <o:p></o:p></p>
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