Help....Extremely large .svs file size won't open

[aSchokman]

Hi guys,

Im new to using both image J and the bio formats plugin. Im trying to analyse some images that have been stored online via the human cancer atlas; however the file sizes for each image range from 500Mb to 1.5Gb. Ive assumed that any regular computer won't have the processing power to open and analyse an image this large and I keep coming up with the following error message (Ive selected to crop on import).

Any insight into the error message, or a possible solution would be great (like booking time on a much more powerful machine if need be).

Cheers,


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ImageJ 1.48v; Java 1.6.0_20 [64-bit]; Windows 7 6.1; 39MB of 3070MB (1%)

java.lang.IllegalArgumentException: Array size too large: 104377 x 78095 x 1
at loci.common.DataTools.safeMultiply32(DataTools.java:854)
at loci.common.DataTools.allocate(DataTools.java:828)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:153)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:313)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:243)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:313)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:313)
at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:190)
at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)
at loci.plugins.in.Importer.readPixels(Importer.java:150)
at loci.plugins.in.Importer.run(Importer.java:89)
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:619)

[mlinkert]

Im new to using both image J and the bio formats plugin. Im trying to analyse some images that have been stored online via the human cancer atlas; however the file sizes for each image range from 500Mb to 1.5Gb. Ive assumed that any regular computer won't have the processing power to open and analyse an image this large and I keep coming up with the following error message (Ive selected to crop on import).

From the error message, it looks like the entire image is still being read. With "Crop on import" selected, do you then see a window that allows you to specify the region of the image to open? If so, what values do you have set in that window? I would expect that setting the width and height of the region to smaller values (e.g. 2048x2048, or even 4096x4096) would work; unfortunately, you won't be able to open the entire image all at once no matter what, as ImageJ cannot display more than 2GB of pixels in a single image plane.

[aSchokman]

Thanks; I got there in the end embarrassingly enough.

Is there any work around to enable bioformats to open more than 2gb of pixels?

Thanks,

[mlinkert]

Is there any work around to enable bioformats to open more than 2gb of pixels?

Unfortunately not; this is not a limitation of Bio-Formats itself, but rather a limitation in Java:

http://en.wikipedia.org/wiki/Criticism_ ... rge_arrays