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<div>Hi. I would like to read in the highest resolution pixel data from a Leica .scn format whole slide fluorescence image and save it in any common format so that I can then work with it in IDL or Matlab. </div>
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<div>I am using Linux (opensuse 13.1) and just downloaded the latest version of ImageJ (1.48v) and installed the latest bioformats imageJ plugin file from today (February 4, 2015). </div>
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<div>I just tried to import the file in ImageJ: ImageJ -> Plugins -> Bio-Formats -> Bio-Formats Importer and got an error "Sorry, there was a problem during import". Here is the log output:</div>
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<div>loci.formats.FormatException: Error setting core metadata for image number 28</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.LeicaSCNReader.initCoreMetadata(LeicaSCNReader.java:241)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.LeicaSCNReader.initStandardMetadata(LeicaSCNReader.java:306)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:95)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:541)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.FormatReader.setId(FormatReader.java:1317)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.Importer.showDialogs(Importer.java:141)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.Importer.run(Importer.java:79)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.LociImporter.run(LociImporter.java:81)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at ij.IJ.runUserPlugIn(IJ.java:199)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at ij.IJ.runPlugIn(IJ.java:163)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at ij.Executer.runCommand(Executer.java:131)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at ij.Executer.run(Executer.java:64)</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.Thread.run(Thread.java:662)</div>
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<div>Am I doing something wrong? Or is it not possible to import this type of file format? Is there any other way I can access this data? </div>
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<div>Thanks so much for your help!</div>
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<div>Best,</div>
<div>Melanie</div>
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