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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi David,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks for your response.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">We’re using Micro Manager 2.0-beta3. I’ve uploaded a sample metadata file – I can see that the formatting is slightly different and this is obviously the cause
of the problem.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Dave.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> ome-users [mailto:ome-users-bounces@lists.openmicroscopy.org.uk]
<b>On Behalf Of </b>David Gault (Staff)<br>
<b>Sent:</b> 23 May 2018 11:48<br>
<b>To:</b> OME User Support List <ome-users@lists.openmicroscopy.org.uk><br>
<b>Subject:</b> Re: [ome-users] Exception thrown when importing Micro Manager dataset with Bioformats<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi David, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Do you know which version of Micro Manager you are using? The formatting of the metadata appears to be different from what the reader in Bio-Formats is expecting, you can see examples of the expected metadata format at <a href="http://downloads.openmicroscopy.org/images/Micro-Manager/">http://downloads.openmicroscopy.org/images/Micro-Manager/</a>.
If you are able to provide a sample file you can submit it to <a href="https://www.openmicroscopy.org/qa2/qa/upload/">https://www.openmicroscopy.org/qa2/qa/upload/</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">With Thanks,<o:p></o:p></p>
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<p class="MsoNormal">David Gault<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<p class="MsoNormal">On 23 May 2018, at 10:30, David Barry <<a href="mailto:David.Barry@crick.ac.uk">David.Barry@crick.ac.uk</a>> wrote:<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:11.0pt;font-family:"Calibri",sans-serif">Hi All,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I’m having an issue importing some Micro manager datasets with Bio Formats. If I select Plugins > Bio-formats > Bio-formats importer and select an OME TIFF file, the image
opens without any issue. However, if I direct bioformats to the metadata.txt file (which, as I understand it, is the recommended approach), the following exception is thrown:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">(Fiji Is Just) ImageJ 2.0.0-rc-65/1.52b; Java 1.8.0_151 [64-bit]; Windows 10 10.0; 441MB of 98162MB (<1%)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">java.lang.NumberFormatException: For input string: ""<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">at java.lang.Integer.parseInt(Integer.java:592)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">at java.lang.Integer.parseInt(Integer.java:615)<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:757)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:433)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">at loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java:297)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">at loci.formats.FormatReader.setId(FormatReader.java:1397)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:499)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">at loci.plugins.in.Importer.showDialogs(Importer.java:140)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">at loci.plugins.in.Importer.run(Importer.java:76)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">at loci.plugins.LociImporter.run(LociImporter.java:78)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">at ij.IJ.runUserPlugIn(IJ.java:222)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">at ij.IJ.runPlugIn(IJ.java:186)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">at ij.Executer.runCommand(Executer.java:137)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">at ij.Executer.run(Executer.java:66)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">at java.lang.Thread.run(Thread.java:748)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Some of my colleagues have reported seeing this exception regardless of whether they point bioformats to the OME TIFF file or the metadata file. Through a little investigation,
I have found that the problem seems to be related to the “UserData” property in the metadata file - deleting this resolves the problem, which leads me to believe that it is not correctly formatted:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“UserData”: {<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“IJType”: {<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“PropVal”: “1”,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“PropType”: “String”<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">},<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“GridRow”: {<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“PropVal”: “”,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">},<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“UUID”: {<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“PropVal”: “b8ff797d-4ca2-4770-bf46-17057f11bad7”,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“PropType”: “String”<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“Height”: {<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“PropVal”: “2048”,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“PropVal”: “0”,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“CameraTimeout”: {<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“KeepShutterOpenChannels”: {<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">},<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“Width”: {<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“PropVal”: “2048”,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“PropType”: “String”<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">},<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“Positions”: {<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“PropVal”: “27”,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“PropType”: “String”<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">},<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“ROI”: {<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“PropVal”: “[0,0,2048,2048]”,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">“PropType”: “String”<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">}<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">}<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">If anyone could shed any light on why micro manager appears to be generating incorrectly formatted metadata files, it would be much appreciated. I have noticed that the bioformats
JARS micro manager uses are somewhat outdated (formats-common-5.1.1.jar, for example), but replacing them with more recent versions seems to cause issues.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Thanks,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Dave.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Lucida Sans",sans-serif;color:gray">Dave Barry,</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Lucida Sans",sans-serif;color:gray">Image Analyst,</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Lucida Sans",sans-serif;color:gray">Crick Advanced Light Microscopy Facility (CALM),</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Lucida Sans",sans-serif;color:gray">The Francis Crick Institute,</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Lucida Sans",sans-serif;color:gray">1 Midland Road,</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Lucida Sans",sans-serif;color:gray">London,</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Lucida Sans",sans-serif;color:gray">NW1 1AT.</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Lucida Sans",sans-serif;color:gray"> </span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Lucida Sans",sans-serif;color:gray">T: +44 20379 60913</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Lucida Sans",sans-serif;color:gray">E:<span class="apple-converted-space"> </span><a href="mailto:david.barry@crick.ac.uk"><span style="color:#0563C1">david.barry@crick.ac.uk</span></a></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Lucida Sans",sans-serif;color:gray">W:<span class="apple-converted-space"> </span><a href="http://www.crick.ac.uk/"><span style="color:#0563C1">www.crick.ac.uk</span></a></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Lucida Sans",sans-serif;color:gray">R: SW312</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;orphans: auto;text-align:start;widows: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<i><span style="font-size:10.0pt;font-family:"Trebuchet MS",sans-serif;color:#707173">The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered
office at 1 Midland Road London NW1 1AT<o:p></o:p></span></i></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
ome-users mailing list<br>
</span><a href="mailto:ome-users@lists.openmicroscopy.org.uk"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#954F72">ome-users@lists.openmicroscopy.org.uk</span></a><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><br>
</span><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#954F72">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</span></a><o:p></o:p></p>
</div>
</blockquote>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal"><br>
<span style="font-size:10.0pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
<o:p></o:p></p>
</div>
<p style="color:rgb(112,113,115);font-family: 'Trebuchet MS', 'Lucida Grande'; font-style: italic; font-size: 10pt;">
The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT</p>
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