[ome-users] .vsi file conversion to .tiff getting exception error

[David Gault (Staff)]

Hi Mousumi,

We received the file you uploaded and I have been able to test it with a number of different Bio-Formats versions. So far I have been unable to reproduce the error you were seeing using the command line tools. Do you know which version of Bio-Formats you are currently using (you can find out by using bfconvert -version)? Are you using any other options or parameters when performing the conversion?

With Thanks,
David Gault

On 20 Jun 2018, at 18:18, Mousumi Roy <mousumi.roy47 at gmail.com<mailto:mousumi.roy47 at gmail.com>> wrote:

Hello David,

I have uploaded the .vsi and supporting files in the link. Kindly let me know if it is accessible properly. Also, I have a request to not to share this image with others.

Thank you,
Mousumi.



On Wed, Jun 20, 2018 at 10:04 AM David Gault (Staff) <d.gault at dundee.ac.uk<mailto:d.gault at dundee.ac.uk>> wrote:
Hi Mousumi,

Thank you for reporting the issue, this is not a bug which we are aware of with VSI, as such it would be good to have a file that reproduces the problem for testing and debugging. If you have a sample file which you can provide for testing you can upload it to https://www.openmicroscopy.org/qa2/qa/upload/

With Thanks,
David Gault

On 19 Jun 2018, at 17:09, Mousumi Roy <mousumi.roy at stonybrook.edu<mailto:mousumi.roy at stonybrook.edu>> wrote:


Hello,

I am using bftools and trying to convert .vsi images into .tiff using  bfconvert command line tool<https://docs.openmicroscopy.org/bio-formats/5.7.1/users/comlinetools/index.html>. But I am getting following error:
Exception in thread "main" loci.formats.FormatException: Plane index:1 must be < 1
at loci.formats.FormatWriter.checkParams(FormatWriter.java:387)
at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:215)
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)

I have 40x .vsi files which I need to convert into .tiff format but it seems I am not able to convert without compression. Kindly assist me.

Thank you. Looking forward to your response.

Sincerely,
Mousumi Roy
Graduate Research assistant
Computer Science
Stony Brook University
m:      6316275860<tel:(631)%20627-5860>
a:      100 Nicolls Rd, Stony Brook, NY 11794<https://maps.google.com/?q=100+Nicolls+Rd,+Stony+Brook,+NY+11794&entry=gmail&source=g>
e:      mousumi.roy at stonybrook.edu<mailto:mousumi.roy at stonybrook.edu>
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