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Hi David,
<div class=""><br class="">
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<div class="">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/" class="">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/" class="">https://www.openmicroscopy.org/qa2/qa/upload/</a></div>
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
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<blockquote type="cite" class="">
<div class="">On 23 May 2018, at 10:30, David Barry <<a href="mailto:David.Barry@crick.ac.uk" class="">David.Barry@crick.ac.uk</a>> wrote:</div>
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Hi All,<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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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 class=""></o:p></div>
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<o:p class=""> </o:p></div>
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(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 class=""></o:p></div>
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<o:p class=""> </o:p></div>
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java.lang.NumberFormatException: For input string: ""<o:p class=""></o:p></div>
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at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
at java.lang.Integer.parseInt(Integer.java:592)<o:p class=""></o:p></div>
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at java.lang.Integer.parseInt(Integer.java:615)<o:p class=""></o:p></div>
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at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:757)<o:p class=""></o:p></div>
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at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:433)<o:p class=""></o:p></div>
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at loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java:297)<o:p class=""></o:p></div>
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at loci.formats.FormatReader.setId(FormatReader.java:1397)<o:p class=""></o:p></div>
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at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:499)<o:p class=""></o:p></div>
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at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)<o:p class=""></o:p></div>
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at loci.plugins.in.Importer.showDialogs(Importer.java:140)<o:p class=""></o:p></div>
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at loci.plugins.in.Importer.run(Importer.java:76)<o:p class=""></o:p></div>
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at loci.plugins.LociImporter.run(LociImporter.java:78)<o:p class=""></o:p></div>
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at ij.IJ.runUserPlugIn(IJ.java:222)<o:p class=""></o:p></div>
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at ij.IJ.runPlugIn(IJ.java:186)<o:p class=""></o:p></div>
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at ij.Executer.runCommand(Executer.java:137)<o:p class=""></o:p></div>
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at ij.Executer.run(Executer.java:66)<o:p class=""></o:p></div>
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at java.lang.Thread.run(Thread.java:748)<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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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 class=""></o:p></div>
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<o:p class=""> </o:p></div>
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“UserData”: {<o:p class=""></o:p></div>
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“IJType”: {<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropVal”: “1”,<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropType”: “String”<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
},<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“GridRow”: {<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropVal”: “0”,<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropType”: “String”<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
},<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“Comment”: {<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropVal”: “”,<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropType”: “String”<o:p class=""></o:p></div>
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},<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“UUID”: {<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropVal”: “b8ff797d-4ca2-4770-bf46-17057f11bad7”,<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropType”: “String”<o:p class=""></o:p></div>
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},<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“Height”: {<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropVal”: “2048”,<o:p class=""></o:p></div>
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“PropType”: “String”<o:p class=""></o:p></div>
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},<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“GridColumn”: {<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropVal”: “0”,<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropType”: “String”<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
},<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“CameraTimeout”: {<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropVal”: “20000”,<o:p class=""></o:p></div>
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“PropType”: “String”<o:p class=""></o:p></div>
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},<o:p class=""></o:p></div>
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“Depth”: {<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropVal”: “2”,<o:p class=""></o:p></div>
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“PropType”: “String”<o:p class=""></o:p></div>
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},<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“BitDepth”: {<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropVal”: “16”,<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropType”: “String”<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
},<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“KeepShutterOpenChannels”: {<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropVal”: “false”,<o:p class=""></o:p></div>
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“PropType”: “String”<o:p class=""></o:p></div>
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},<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PixelType”: {<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropVal”: “GRAY16”,<o:p class=""></o:p></div>
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“PropType”: “String”<o:p class=""></o:p></div>
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},<o:p class=""></o:p></div>
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“Source”: {<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropVal”: “Micro-Manager”,<o:p class=""></o:p></div>
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“PropType”: “String”<o:p class=""></o:p></div>
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},<o:p class=""></o:p></div>
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“TimeFirst”: {<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropVal”: “false”,<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropType”: “String”<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
},<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“ChColors”: {<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropVal”: “[-1,-13382401,-65536,-16711834]”,<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropType”: “String”<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
},<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“SlicesFirst”: {<o:p class=""></o:p></div>
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“PropVal”: “false”,<o:p class=""></o:p></div>
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“PropType”: “String”<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
},<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“Width”: {<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropVal”: “2048”,<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropType”: “String”<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
},<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“Positions”: {<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropVal”: “27”,<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropType”: “String”<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
},<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“ROI”: {<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropVal”: “[0,0,2048,2048]”,<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
“PropType”: “String”<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
}<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
}<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
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 class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Thanks,<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Dave.<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" style="font-size: 10pt; font-family: 'Lucida Sans', sans-serif; color: gray;" class="">Dave Barry,<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" style="font-size: 10pt; font-family: 'Lucida Sans', sans-serif; color: gray;" class="">Image Analyst,<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" style="font-size: 10pt; font-family: 'Lucida Sans', sans-serif; color: gray;" class="">Crick Advanced Light Microscopy Facility (CALM),<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" style="font-size: 10pt; font-family: 'Lucida Sans', sans-serif; color: gray;" class="">The Francis Crick Institute,<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" style="font-size: 10pt; font-family: 'Lucida Sans', sans-serif; color: gray;" class="">1 Midland Road,<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" style="font-size: 10pt; font-family: 'Lucida Sans', sans-serif; color: gray;" class="">London,<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" style="font-size: 10pt; font-family: 'Lucida Sans', sans-serif; color: gray;" class="">NW1 1AT.<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" style="font-size: 10pt; font-family: 'Lucida Sans', sans-serif; color: gray;" class=""> </span></div>
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<span lang="EN-GB" style="font-size: 10pt; font-family: 'Lucida Sans', sans-serif; color: gray;" class="">T: +44 20379 60913<o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-size: 10pt; font-family: 'Lucida Sans', sans-serif; color: gray;" class="">E:<span class="Apple-converted-space"> </span><a href="mailto:david.barry@crick.ac.uk" style="color: rgb(149, 79, 114); text-decoration: underline;" class=""><span style="color: rgb(5, 99, 193);" class="">david.barry@crick.ac.uk</span></a><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-size: 10pt; font-family: 'Lucida Sans', sans-serif; color: gray;" class="">W:<span class="Apple-converted-space"> </span><a href="http://www.crick.ac.uk/" style="color: rgb(149, 79, 114); text-decoration: underline;" class=""><span style="color: rgb(5, 99, 193);" class="">www.crick.ac.uk</span></a><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-size: 10pt; font-family: 'Lucida Sans', sans-serif; color: gray;" class="">R: SW312<o:p class=""></o:p></span></div>
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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>
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">ome-users
mailing list</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">ome-users@lists.openmicroscopy.org.uk</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a></div>
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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