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<div>Hi Ewan,</div>
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<div>Thank you for submitting your file.</div>
<div>We were able to reproduce the bug locally.</div>
<div><br>
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<div>A ticket has been created on this regard,</div>
<div>https://trac.openmicroscopy.org/ome/ticket/13002,</div>
<div>and you have been added to the cc list.</div>
<div><br>
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<div>Notifications will be sent to your email id, when there is a status change on the ticket.</div>
<div><br>
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<div>Best,</div>
<div>Balaji </div>
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<div style="color: rgb(40, 40, 40);"><span style="background-color: rgb(255, 255, 255);">__________________</span></div>
<div style="color: rgb(40, 40, 40);">
<p style="margin-top: 0px; margin-bottom: 0px;">Mr Balaji Ramalingam</p>
<p style="margin-top: 0px; margin-bottom: 0px;">Software Developer<br>
</p>
<p style="margin-top: 0px; margin-bottom: 0px;">OME Team</p>
<p style="margin-top: 0px; margin-bottom: 0px;">College of Life Sciences</p>
<p style="margin-top: 0px; margin-bottom: 0px;">University of Dundee</p>
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<span style="font-weight:bold">From: </span><Munro>, Ian <<a href="mailto:i.munro@imperial.ac.uk">i.munro@imperial.ac.uk</a>><br>
<span style="font-weight:bold">Reply-To: </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Date: </span>Friday, 21 August 2015 14:29<br>
<span style="font-weight:bold">To: </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ome-users] Imspector msr FLIM<br>
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Hi Ewan
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<div>I can confirm that I am able to reproduce both issues with the current version of FLIMfit.</div>
<div><br>
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<div>I have also imported the file which opens - “ 02 - 70 - 1 - tp1 - x16 TCSPC.msr” to the server on
<a href="http://demo.openmicroscopy.org">demo.openmicroscopy.org</a></div>
<div>where the attached ModuloAlong annotation has the same incorrect 1ps time axis.</div>
<div><br>
</div>
<div>Running the Bio-Formats showinf command on the other file "01 - 770nm FITC - HybridPMT.msr” gives me the same error</div>
<div><br>
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<div>ImspectorReader initializing 01-770nm FITC-HybridPMT.msr</div>
<div>Exception in thread "main" java.lang.ArithmeticException: / by zero</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.ImspectorReader.initFile(ImspectorReader.java:421)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.FormatReader.setId(FormatReader.java:1426)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.ImageReader.setId(ImageReader.java:835)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1013)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.tools.ImageInfo.main(ImageInfo.java:1102)</div>
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<div><br>
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<div>This suggests that in both cases the issues arise from the Bio-Formats reader rather than FLIMfit or the Matlab interface.</div>
<div>Would it be possible for someone from the Bio-Formats team to confirm this please?</div>
<div><br>
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<div>Regards</div>
<div><br>
</div>
<div>Ian</div>
<div><br>
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<div><br>
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<div>On 21 Aug 2015, at 12:26, Ewan McGhee <<a href="mailto:e.mcghee@beatson.gla.ac.uk">e.mcghee@beatson.gla.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 14px; font-family: Calibri, sans-serif;">
<div>Hi,</div>
<div><br>
</div>
<div>I believe I’ve encountered a problem trying to use the raw msr files produced by our LaVision Biotec Trim-scopes – specifically, the FLIM data that we acquire.</div>
<div><br>
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<div>There seems to be two separate problems:</div>
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<div><span class="Apple-tab-span" style="white-space:pre"></span>1. The data taken on the old Trim-scope which runs 32-bit Imspector and uses the LaVisionBiotec x16-TCSPC detector, loads into FLIMFit but the time axis used for measuring the decay is wrong (it
shows as 0 to 1 ps, when it should be 0 to 12 ns). The one-tiff export produced by Imspector of the same data, however, loads fine with the correct time axis values. </div>
<div><br>
</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>2. The new Trim-scope we have runs the 64-bit version of Imspector as we have the new hybrid PMT FLIM detectors on this. The msr file produced form this system just crashes out completely - </div>
<div><br>
</div>
<div>
<div>Error using flim_data_series/get_image_dimensions (line 108)</div>
<div>Java exception occurred: </div>
<div>java.lang.ArithmeticException: / by zero</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.ImspectorReader.initFile(ImspectorReader.java:421)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.FormatReader.setId(FormatReader.java:1426)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.ImageReader.setId(ImageReader.java:835)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289).</div>
</div>
<div><br>
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<div>I have uploaded an example of each data file to <a href="https://www.openmicroscopy.org/qa2/qa/upload/" style="font-size: 12px; font-family: Calibri;">https://www.openmicroscopy.org/qa2/qa/upload/</a>, with the detector type indicated in the file name: 01
- 770nm FITC - HybridPMT.msr and 02 - 70 - 1 - tp1 - x16 TCSPC.msr.</div>
<div><br>
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<div>If I can help any other way just let me know.</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Ewan</div>
</div>
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