Reading .spl file with matlab
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I downloaded the Open Microscopy Environment functions so I can import my data into matlab rather than having to export each file manually using our microscope's software. I installed the loci_tools.jar and I was able to import one file with minor problems--it was not able to correctly sort out the channels, Z planes, and time points but I figured out the pattern for the mistakes and was able to easily work around them. Then I tried on another file and I got an error message.
This is the error that I got:
I = bfopen(‘filename.spl’);
Finding offsets to pixel data
Determining dimensions
Reading series #1
.Error using loci.formats.ChannelSeparator/openBytes
Java exception occurred:
java.lang.IllegalArgumentException: Negative position
at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:600)
at
loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:133)
at loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:118)
at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:532)
at loci.common.NIOFileHandle.seek(NIOFileHandle.java:254)
at loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:140)
at loci.formats.in.SlidebookReader.openBytes(SlidebookReader.java:130)
at loci.formats.ImageReader.openBytes(ImageReader.java:414)
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:197)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:226)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:159)
Error in bfGetPlane (line 75)
plane = r.openBytes(iPlane - 1, ip.Results.x - 1, ip.Results.y - 1, ...
Error in bfopen (line 144)
arr = bfGetPlane(r, i, varargin{:});
The .spl file was made using Slidebook v4.2 and I am using Matlab 2011b on a Mac with the image processing toolbox among others.
Any ideas as for what I should do would be greatly appreciated
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