[ome-users] Bug report concerning .vsi files

[Johannes Koch]

Dear OME Team,

using ImageJ 1.47c, Java 1.6.0_20 under Win7 64-bit SP1, I am trying to 
open .vsi formats acquired on Olympus CellSense 1.7 using LOCI 4.4.4.

These are my first .vsi images and I recorded beads. When opening the 
"blue" beads image, almost everything is fine. I run the importer, 
select my .vsi file, and then get two image stacks to select, where 
there is indeed only a single one (compare screenshot folder vs 
screenshot import list). However, I ignore the second and it opens fine. 
No metadata is available which is a pity, but I relegate this to Olympus?!

When I want to open the "green" beads image, an exception is thrown (see 
screenshot).

When I think about it, it must be the image header - the only difference 
is the wavelength, which is for sure written in the metadata. Apart from 
this, the images are identically acquired. As no metadata is displayed 
(for the "blue"), multiple stacks are shown where there is only one 
("blue") and a  Tags error pops up (for the "green"), the header might 
not be understood properly. It should be emphasized that I run CellSense 
1.7, which is the newer software. I dont have hands on the 1.6 version, 
but maybe they changed something.

I dont have data attached since it would be several hundreds of MB- if 
you supply me with an upload link, I could give you some example files.

Thanks
Johannes

-- 

*Dr. Johannes Koch*

*Tissue Med Biosciences GmbH*

Magnesitstrasse1 | A-3500 Krems

T: +43/2732/87470-300 | M: jk at tmbiosciences.com 
<mailto:jk at tmbiosciences.com>

*www.tmbiosciences.com <http://www.tmbiosciences.com/>*

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java.lang.IllegalArgumentException: Negative position

	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:610)

	at loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:120)

	at loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:105)

	at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:510)

	at loci.common.NIOFileHandle.seek(NIOFileHandle.java:232)

	at loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:104)

	at loci.formats.in.CellSensReader.readTags(CellSensReader.java:648)

	at loci.formats.in.CellSensReader.readTags(CellSensReader.java:685)

	at loci.formats.in.CellSensReader.readTags(CellSensReader.java:685)

	at loci.formats.in.CellSensReader.readTags(CellSensReader.java:685)

	at loci.formats.in.CellSensReader.initFile(CellSensReader.java:299)

	at loci.formats.FormatReader.setId(FormatReader.java:1072)

	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:481)

	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)

	at loci.plugins.in.Importer.showDialogs(Importer.java:125)

	at loci.plugins.in.Importer.run(Importer.java:77)

	at loci.plugins.LociImporter.run(LociImporter.java:79)

	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:619)

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