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

[Mousumi Roy]

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>
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> 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>
> 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
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>>>
>>>
>>>
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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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