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

[Mousumi Roy]

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>
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> 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>
> 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> 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 <(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
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
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>>
>>
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
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