showinf on vsi gives IllegalArgumentException

[jrowell]

I am having a problem with some vsi files that I just received. I am using showinf from bftools.zip downloaded from the website and loci_tools.jar 4.4.4 (I have tried the stable, trunk and daily builds).

If I do the following:

showinf -nopix my.vsi

I get:

Checking file format [CellSens VSI]
Initializing reader
Exception in thread "main" java.lang.IllegalArgumentException
at java.nio.Buffer.position(Buffer.java:216)
at ome.scifio.io.NIOFileHandle.buffer(NIOFileHandle.java:538)
at ome.scifio.io.NIOFileHandle.seek(NIOFileHandle.java:257)
at ome.scifio.io.RandomAccessInputStream.seek(RandomAccessInputStream.java:143)
at loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:108)
at loci.formats.in.CellSensReader.readTags(CellSensReader.java:785)
at loci.formats.in.CellSensReader.readTags(CellSensReader.java:826)
at loci.formats.in.CellSensReader.readTags(CellSensReader.java:826)
at loci.formats.in.CellSensReader.readTags(CellSensReader.java:826)
at loci.formats.in.CellSensReader.readTags(CellSensReader.java:826)
at loci.formats.in.CellSensReader.readTags(CellSensReader.java:826)
at loci.formats.in.CellSensReader.readTags(CellSensReader.java:826)
at loci.formats.in.CellSensReader.initFile(CellSensReader.java:355)
at loci.formats.FormatReader.setId(FormatReader.java:1178)
at loci.formats.ImageReader.setId(ImageReader.java:729)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:530)
at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1003)
at loci.formats.tools.ImageInfo.main(ImageInfo.java:1048)

Any idea how I can resolve this problem?

[cxallan]

We'd love to help but to do so we really need the data.

You should be able to upload the file to OMERO.qa:

https://www.openmicroscopy.org/qa2/qa/upload/

We will send alternate instructions in a private message in case that does not work.

[jrowell]

Thank you for the reply. I tried to use the upload tool to post my image but it doesn't look like vsi is an accepted file format. Please PM me with instructions on how I can get the data to you.