<div dir="ltr">Hi Alan,<br><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Nov 18, 2015 at 3:41 PM, Alan Race <span dir="ltr"><<a href="mailto:alan.race@npl.co.uk" target="_blank">alan.race@npl.co.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">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.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">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></p></div></div></blockquote><div><br></div><div>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:12.8px">exposed some limitations in the existing clients when handling data with such a large number of channels. And second </span><span style="font-size:12.8px">with m/z along the time dimension and a FLIM style annotation </span><span style="font-size:12.8px">to show what mass spec data might look like if a FLIMfit style client were written.</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">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></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Hopefully you and yours enjoy the time (one way or the other) until then!</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">~Josh.</span></div><div><br></div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div lang="EN-GB" link="blue" vlink="purple"><div>
<p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Regards,</span><span style="color:rgb(31,73,125);font-family:Calibri,sans-serif;font-size:11pt"> </span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Alan<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"><u></u> <u></u></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"> Munro, Ian [mailto:<a href="mailto:i.munro@imperial.ac.uk" target="_blank">i.munro@imperial.ac.uk</a>]
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<b>Sent:</b> 18 November 2015 14:33<span class=""><br>
<b>To:</b> Alan Race <<a href="mailto:alan.race@npl.co.uk" target="_blank">alan.race@npl.co.uk</a>><br>
<b>Cc:</b> <a href="mailto:p.walczysko@dundee.ac.uk" target="_blank">p.walczysko@dundee.ac.uk</a>; <a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.openmicroscopy.org.uk</a><br>
<b>Subject:</b> Re: [ome-devel] Spectral Chemical Imaging Data<u></u><u></u></span></span></p>
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<p class="MsoNormal">Thanks Alan <u></u><u></u></p><div><div class="h5">
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<p class="MsoNormal">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 <u></u><u></u></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.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></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.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Regards<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Ian <u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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