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

Mon Jun 25 10:19:46 BST 2018

Hi Mousumi,

I was simply using the standard command with no extra options:
bfconvert /path/to/input.vsi output.tiff

If you are seeing issues with the memory then you can also increase it by setting BF_MAX_MEM as below:
Mac/Linux:     export BF_MAX_MEM=4G
Windows: set BF_MAX_MEM=4G

With Thanks,
David Gault

On 23 Jun 2018, at 05:15, Mousumi Roy <mousumi.roy47 at gmail.com<mailto:mousumi.roy47 at gmail.com>> wrote:

Hi David,

Even after upgrading the Bio-format I am still not able to convert the vsi to tiff. Can you kindly specify how you are converting the vsi files? What command are you using? Even after increasing heap memory, I am getting java heap memory exception.

Thank you,
Mousumi.

On Fri, Jun 22, 2018 at 6:27 AM David Gault (Staff) <d.gault at dundee.ac.uk<mailto:d.gault at dundee.ac.uk>> wrote:
Hi Mousumi,

Thank you for providing those details. With the provided sample file I am still unable to reproduce the same error using version 5.5.2.

I would recommend updating to the latest Bio-Formats 5.8.2 as there have been improvements to that reader in the past number of months. If that does not fix the issue then we would likely need an additional sample file which can be used to reproduce the error, as before it can be uploaded to https://www.openmicroscopy.org/qa2/qa/upload/

With Thanks,
David Gault

On 21 Jun 2018, at 19:44, Mousumi Roy <mousumi.roy47 at gmail.com<mailto:mousumi.roy47 at gmail.com>> wrote:

Hi David,

Thank you for your reply.

Version: 5.5.2

Build date: 15 June 2017

VCS revision: 4c2f2b00a12aa8a3894c54459a4cf02d5b02e161

I am using the command:

../../bftools/bfconvert S34146_A1-Aromatase_01.vsi output.tiff

(not anything else) and I am getting the following error:

S34146_A1-Aromatase_01.vsi

CellSensReader initializing S34146_A1-Aromatase_01.vsi

[CellSens VSI] -> output.tiff [Tagged Image File Format]

Switching to BigTIFF (by file size)

Tile size = 512 x 512

Exception in thread "main" java.lang.NullPointerException

at java.lang.System.arraycopy(Native Method)

at loci.formats.in.CellSensReader.openBytes(CellSensReader.java:538)

at loci.formats.FormatReader.openBytes(FormatReader.java:886)

at loci.formats.ImageReader.openBytes(ImageReader.java:441)

at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:698)

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 no clue howo should I fix this exception. Looking for your help.

Thank you,

Mousumi.

On Thu, Jun 21, 2018 at 6:18 AM David Gault (Staff) <d.gault at dundee.ac.uk<mailto:d.gault at dundee.ac.uk>> wrote:
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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