[ome-users] Bug report concerning .vsi files

[Melissa Linkert]

Hi Johannes,

Thank you for sending an example dataset.

Unfortunately (or maybe fortunately!), that dataset does open correctly
for me with Bio-Formats 4.4.4.  Could you please check that ImageJ is in
fact using the 4.4.4 version of Bio-Formats ("Help > About Plugins >
LOCI Plugins" should tell you the version number)?

If ImageJ is not using 4.4.4, then please try removing all copies of
loci_tools.jar from your plugins folder and download a fresh copy from:

http://loci.wisc.edu/bio-formats/downloads

If ImageJ is definitely using 4.4.4 and you see the same error message,
then please let us know.

Regards,
-Melissa

On Mon, Oct 22, 2012 at 08:52:42AM -0400, Melissa Linkert wrote:
> 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/>*
> > 
> > Diese E-Mail enthält vertrauliche und/oder rechtlich geschützte
> > Information. Wenn Sie nicht der richtige Adressat sind oder diese
> > E-Mail irrtümlich erhalten haben, informieren Sie bitte unverzüglich
> > den Absender und vernichten Sie diese E-Mail sofort. Das unerlaubte
> > Kopieren sowie die unbefugte Weitergabe dieser E-Mail sind nicht
> > gestattet.
> > 
> > This e-mail may contain confidential and/or privileged information.
> > If you are not the intended recipient or have received this e-mail
> > in error please notify the sender immediately and destroy this
> > e-mail. Any unauthorized copying, disclosure or distribution of the
> > material in this e-mail is strictly forbidden.
> > 
> 
> > 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)
> 
> 
> 
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>