[ome-users] Error when converting large .svs or .vsi images

[Tarbox, Lawrence]

In converting large .svs or .vsi images, I get the following error:

/home/ltarbox/CIR-scans
54680.svs
SVSReader initializing 54680.svs
Reading IFDs
Populating metadata
Populating OME metadata
[Aperio SVS] -> /home/ltarbox/CIR-scans/out/WSI-2_S%s.ome.tif [OME-TIFF]
Switching to BigTIFF (by file size)
Tile size = 256 x 256
Exception in thread "main" java.lang.IllegalArgumentException
        at java.nio.Buffer.limit(Buffer.java:275)
        at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:636)
        at loci.common.NIOFileHandle.writeSetup(NIOFileHandle.java:642)
        at loci.common.NIOFileHandle.write(NIOFileHandle.java:505)
        at loci.common.NIOFileHandle.write(NIOFileHandle.java:499)
        at loci.common.NIOFileHandle.write(NIOFileHandle.java:487)
        at loci.common.RandomAccessOutputStream.write(RandomAccessOutputStream.java:217)
        at loci.formats.tiff.TiffSaver.writeIFDStrips(TiffSaver.java:987)
        at loci.formats.tiff.TiffSaver.writeImageIFD(TiffSaver.java:451)
        at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:401)
        at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:277)
        at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:275)
        at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:218)
        at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:748)
        at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:634)
        at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:563)
        at loci.formats.tools.ImageConverter.main(ImageConverter.java:884)

Smaller images convert fine.

I tripled the memory size (to 40 GB), but it stll fails

Ideas?

Lawrence Tarbox, Ph.D., Dept. of Biomedical Informatics, Univ. of Arkansas for Medical Sciences
mailto:LTarbox at uams.edu +1.314.681-2752

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