[ome-users] Bug report concerning .vsi files

[Melissa Linkert]

Hi Johannes,

> 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?!

The second image is expected - .vsi datasets almost always have the
"real" image that you acquired, plus a thumbnail image.

> 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.

You are almost certainly correct that there is some small difference in
the header.  If you could send one of the "green" datasets, that would
be very helpful; I will send instructions in a private mail.

Regards,
-Melissa

On Mon, Oct 22, 2012 at 10:46:47AM +0200, Johannes Koch wrote:
> 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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