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Dear Melanie,
<div><br>
</div>
<div>The error you pasted below suggest at a potential bug in Bio-Formats. Would you be willing to</div>
<div>upload a sample file at:</div>
<div><a href="http://qa.openmicroscopy.org.uk/qa/upload/">http://qa.openmicroscopy.org.uk/qa/upload/</a></div>
<div><br>
</div>
<div>
<div>As a side note, you should be able to work against your Leica SCN files directly in IDL</div>
<div>or MATLAB, i.e. without having to convert them. See:</div>
<div>- the example scripts from Karsten Rodenacker for IDL</div>
<div><a href="https://www.openmicroscopy.org/site/support/bio-formats5/users/idl/index.html">https://www.openmicroscopy.org/site/support/bio-formats5/users/idl/index.html</a></div>
<div>- the documentation page on the Bio-Formats MATLAB toolbox</div>
<div><a href="https://www.openmicroscopy.org/site/support/bio-formats5/developers/matlab-dev.html">https://www.openmicroscopy.org/site/support/bio-formats5/developers/matlab-dev.html</a></div>
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<div><br>
</div>
<div>Best,</div>
<div>Sebastien
<div><br>
<div>
<div>On 4 Feb 2015, at 14:16, Freed, Melanie <<a href="mailto:Melanie.Freed@nyumc.org">Melanie.Freed@nyumc.org</a>> wrote:</div>
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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>
<div><br>
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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>
<div><br>
</div>
<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>
<div><br>
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<div>----------</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>
</div>
<div>----------</div>
<div><br>
</div>
<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>
<div><br>
</div>
<div>Thanks so much for your help!</div>
<div><br>
</div>
<div>Best,</div>
<div>Melanie</div>
<div><br>
</div>
</div>
<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;">_______________________________________________</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;">
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<br>
<div><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px;"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">
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<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical School</div>
<div>Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div>College of Life Sciences, University of Dundee, Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK Tel: (01382) 386364</div>
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<br>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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