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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">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.<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">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.<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">Regards,<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>
<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"> Munro, Ian [mailto:i.munro@imperial.ac.uk]
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<b>Sent:</b> 18 November 2015 14:33<br>
<b>To:</b> Alan Race <alan.race@npl.co.uk><br>
<b>Cc:</b> p.walczysko@dundee.ac.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">Thanks Alan <o:p></o:p></p>
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<p class="MsoNormal">I’ve started experimenting using this software <a href="http://www4.ncsu.edu/~dcmuddim/msireader.html">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">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"><o:p> </o:p></p>
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<p class="MsoNormal">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"><o:p> </o:p></p>
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<p class="MsoNormal">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"><o:p> </o:p></p>
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