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<p class="MsoNormal"><span style="color:#1F497D">Hi everyone,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Further to my previous email, I have now uploaded 2 x datasets. The one that I can open is called #12.msr. The one I can’t open is called Brain_01.msr<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Kind regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Jacqui<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="mso-fareast-language:EN-NZ">From:</span></b><span lang="EN-US" style="mso-fareast-language:EN-NZ"> Jacqueline Ross
<br>
<b>Sent:</b> Thursday, 8 March 2018 12:29 p.m.<br>
<b>To:</b> 'ome-users@lists.openmicroscopy.org.uk' <ome-users@lists.openmicroscopy.org.uk><br>
<b>Subject:</b> Abberior MSR files - having trouble opening them with Fiji and ImageJ<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoPlainText">Hi everyone,<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">I'm having trouble opening some MSR files acquired on an Abberior STED system. Some are opening but others aren't and I get the error shown below in those cases. I updated my Fiji version and also tried putting the latest version of
Bioformats in ImageJ to no avail. Some of these will be z stacks but not all.<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Interestingly, it is all of the files we acquired later that we can’t open. The first ones were fine. I’m not sure if the first one we can’t open is a z-stack and if that somehow has caused a problem with the rest. We don’t have the
Abberior system here so don’t have the original software available to open the files. I will upload some files but can’t provide metadata or screenshots for the problem files as I can’t open them with Fiji and don’t have the original data. I will upload one
file that I can open together with its metadata.<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">I am running the latest Fiji version (ImageJ 1.51u) with Bio-Formats Release 5.8.1 – see attached screenshots. I also couldn’t open these files with an older compilation or on our Mac so I don’t think it’s platform-specific. I am using
a 64bit Windows computer with Java 1.8.<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Can anyone help? It would be very much appreciated.<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">(Fiji Is Just) ImageJ 2.0.0-rc-65/1.51u; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 66MB of 100000MB (<1%)<o:p></o:p></p>
<p class="MsoPlainText">java.lang.IllegalArgumentException: 0 must not be null and positive.<o:p></o:p></p>
<p class="MsoPlainText"> at ome.xml.model.primitives.PositiveInteger.<init>(<o:p></o:p></p>
<p class="MsoPlainText">PositiveInteger.java:48)<o:p></o:p></p>
<p class="MsoPlainText"> at loci.formats.MetadataTools.populatePixelsOnly(<o:p></o:p></p>
<p class="MsoPlainText">MetadataTools.java:288)<o:p></o:p></p>
<p class="MsoPlainText"> at loci.formats.MetadataTools.populateMetadata(<o:p></o:p></p>
<p class="MsoPlainText">MetadataTools.java:251)<o:p></o:p></p>
<p class="MsoPlainText"> at loci.formats.MetadataTools.<o:p></o:p></p>
<p class="MsoPlainText">populatePixels(MetadataTools.java:151)<o:p></o:p></p>
<p class="MsoPlainText"> at loci.formats.MetadataTools.<o:p></o:p></p>
<p class="MsoPlainText">populatePixels(MetadataTools.java:97)<o:p></o:p></p>
<p class="MsoPlainText"> at loci.formats.in.OBFReader.initFile(OBFReader.java:217)<o:p></o:p></p>
<p class="MsoPlainText"> at loci.formats.FormatReader.setId(FormatReader.java:1397)<o:p></o:p></p>
<p class="MsoPlainText"> at loci.plugins.in.ImportProcess.<o:p></o:p></p>
<p class="MsoPlainText">initializeFile(ImportProcess.java:499)<o:p></o:p></p>
<p class="MsoPlainText"> at loci.plugins.in.ImportProcess.<o:p></o:p></p>
<p class="MsoPlainText">execute(ImportProcess.java:142)<o:p></o:p></p>
<p class="MsoPlainText"> at loci.plugins.in.Importer.showDialogs(Importer.java:140)<o:p></o:p></p>
<p class="MsoPlainText"> at loci.plugins.in.Importer.run(Importer.java:76)<o:p></o:p></p>
<p class="MsoPlainText"> at loci.plugins.LociImporter.run(LociImporter.java:78)<o:p></o:p></p>
<p class="MsoPlainText"> at ij.IJ.runUserPlugIn(IJ.java:221)<o:p></o:p></p>
<p class="MsoPlainText"> at ij.IJ.runPlugIn(IJ.java:185)<o:p></o:p></p>
<p class="MsoPlainText"> at ij.IJ.runPlugIn(IJ.java:174)<o:p></o:p></p>
<p class="MsoPlainText"> at HandleExtraFileTypes.openImage(<o:p></o:p></p>
<p class="MsoPlainText">HandleExtraFileTypes.java:499)<o:p></o:p></p>
<p class="MsoPlainText"> at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)<o:p></o:p></p>
<p class="MsoPlainText"> at ij.IJ.runUserPlugIn(IJ.java:221)<o:p></o:p></p>
<p class="MsoPlainText"> at ij.IJ.runPlugIn(IJ.java:185)<o:p></o:p></p>
<p class="MsoPlainText"> at ij.IJ.runPlugIn(IJ.java:174)<o:p></o:p></p>
<p class="MsoPlainText"> at ij.io.Opener.openWithHandleExtraFileTypes(<o:p></o:p></p>
<p class="MsoPlainText">Opener.java:515)<o:p></o:p></p>
<p class="MsoPlainText"> at ij.io.Opener.openImage(Opener.java:369)<o:p></o:p></p>
<p class="MsoPlainText"> at ij.io.Opener.openImage(Opener.java:242)<o:p></o:p></p>
<p class="MsoPlainText"> at ij.io.Opener.open(Opener.java:109)<o:p></o:p></p>
<p class="MsoPlainText"> at ij.io.Opener.openAndAddToRecent(Opener.java:291)<o:p></o:p></p>
<p class="MsoPlainText"> at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)<o:p></o:p></p>
<p class="MsoPlainText"> at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)<o:p></o:p></p>
<p class="MsoPlainText"> at java.lang.Thread.run(Thread.java:745)<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Kind regards,<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Jacqui<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#1F497D;mso-fareast-language:EN-NZ">Jacqueline Ross<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#1F497D;mso-fareast-language:EN-NZ">Biomedical Imaging Microscopist<br>
Biomedical Imaging Research Unit (BIRU)<br>
School of Medical Sciences <br>
Faculty of Medical & Health Sciences <br>
The University of Auckland <br>
Private Bag 92019 <br>
Auckland 1142, NEW ZEALAND <br>
<br>
Telephone: Ext 87438; DDI: +64 9 923 7438 <br>
<br>
Website: <a href="http://www.auckland.ac.nz/biru"><span style="color:blue">http://www.auckland.ac.nz/biru</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#1F497D;mso-fareast-language:EN-NZ"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#1F497D;mso-fareast-language:EN-NZ"><o:p> </o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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