Open Microscopy Environment

I have an SLD file that I am trying to load using Matlab and Bioformats. When I do this

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>> img = bfopen( 'devin.sld' );
Error using loci.formats.ChannelSeparator/setId
Java exception occurred:
loci.formats.UnknownFormatException: Unknown file format: /Users/icaoberg/Desktop/devin.sld
   at loci.formats.ImageReader.getReader(ImageReader.java:192)
   at loci.formats.ImageReader.setId(ImageReader.java:727)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
   at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
   at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)

Error in bfGetReader (line 80)
r.setId(id);
Error in bfopen (line 116)
r = bfGetReader(id, stitchFiles);


I understand Bioformats is saying it is an unknown file format, but I would like to know if this is either a known issue with Bioformats or a problem with my actual file. I understand from the docs that it may fail reading the metadata, but I am only interested in the pixel values.

I tried to the same with the ImageJ plugin and get a similar error

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loci.formats.UnknownFormatException: Unknown file format: /Users/icaoberg/Desktop/devin.sld
   at loci.formats.ImageReader.getReader(ImageReader.java:192)
   at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:596)
   at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:472)
   at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
   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:185)
   at ij.IJ.runPlugIn(IJ.java:152)
   at ij.Executer.runCommand(Executer.java:127)
   at ij.Executer.run(Executer.java:64)
   at java.lang.Thread.run(Thread.java:680)
loci.formats.UnknownFormatException: Unknown file format: /Users/icaoberg/Desktop/devin.sld
   at loci.formats.ImageReader.getReader(ImageReader.java:192)
   at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:596)
   at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:472)
   at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
   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:185)
   at ij.IJ.runPlugIn(IJ.java:152)
   at ij.Executer.runCommand(Executer.java:127)
   at ij.Executer.run(Executer.java:64)
   at java.lang.Thread.run(Thread.java:680)


It is a very big file, I don't know what could be the issue.

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(Canopy 32bit) Ivans-MacBook-Pro-2:Desktop icaoberg$ du -h devin.sld
9.0G   devin.sld


Any feedback would be appreciated.

Hi Ivan,

There was a ticket for something similar:

http://trac.openmicroscopy.org.uk/ome/ticket/10473

but it should have been fixed in 4.4.7 and later. Which version of Bio-Formats do you have installed in Matlab and/or ImageJ?

-Melissa

Check out this guide for loading bio-images in MATLAB, see if it helps:
http://imageprocessingblog.com/importing-generic-bioimage-files-to-matlab/