[ome-users] Problem reading Leica .scn image (opensuse 13.1/ImageJ 1.48v/Bioformats Feb 4, 2015)

[Sebastien Besson (Staff)]

Dear Melanie,

The error you pasted below suggest at a potential bug in Bio-Formats. Would you be willing to
upload a sample file at:
http://qa.openmicroscopy.org.uk/qa/upload/

As a side note, you should be able to work against your Leica SCN files directly in IDL
or MATLAB, i.e. without having to convert them. See:
- the example scripts from Karsten Rodenacker for IDL
https://www.openmicroscopy.org/site/support/bio-formats5/users/idl/index.html
- the documentation page on the Bio-Formats MATLAB toolbox
https://www.openmicroscopy.org/site/support/bio-formats5/developers/matlab-dev.html

Best,
Sebastien

On 4 Feb 2015, at 14:16, Freed, Melanie <Melanie.Freed at nyumc.org<mailto:Melanie.Freed at nyumc.org>> wrote:


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.

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).

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:

----------
loci.formats.FormatException: Error setting core metadata for image number 28
at loci.formats.in.LeicaSCNReader.initCoreMetadata(LeicaSCNReader.java:241)
at loci.formats.in.LeicaSCNReader.initStandardMetadata(LeicaSCNReader.java:306)
at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:95)
at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:541)
at loci.formats.FormatReader.setId(FormatReader.java:1317)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
at loci.plugins.in.Importer.showDialogs(Importer.java:141)
at loci.plugins.in.Importer.run(Importer.java:79)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:199)
at ij.IJ.runPlugIn(IJ.java:163)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:662)
----------

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?

Thanks so much for your help!

Best,
Melanie

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Dr Sébastien Besson
Open Microscopy Environment / Harvard Medical School
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364


The University of Dundee is a registered Scottish Charity, No: SC015096
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