[ome-users] Crop on import with Nikon ND2 image files - Only works with x-origin=1

[Enno R. Oldewurtel]

Hi Sebastien,
the 5.0.2-DEV version you pointed me to works and bfopen returns a
correctly cropped image.
Best wishes,
Enno


On Mon, Jul 28, 2014 at 2:19 PM, Sebastien Besson <seb.besson at gmail.com>
wrote:

> Hi Enno,
>
> thanks for the quick upload. I have been able to reproduce the bug you saw
> using MATLAB
> and Bio-Formats 5.0.2 and I can confirm the 5.0.3 release candidate should
> fix  this issue with
> the tile correctly loaded.
>
> You can either wait for the imminent 5.0.3 release of try out one of the
> non-release
> quality continuous integration artifacts from:
>
> http://ci.openmicroscopy.org/job/BIOFORMATS-5.0-latest/lastSuccessfulBuild/artifact/artifacts/
>
> Best regards,
> Sebastien
>
> On 28 Jul 2014, at 13:10, Enno R. Oldewurtel <enno.oldewurtel at uni-koeln.de>
> wrote:
>
> Hey Sebastien,
>
> I used the 5.0.2 release. I uploaded a nd2 file as requested
>
> http://qa.openmicroscopy.org.uk/qa/feedback/9422/?token=f74e8565db4a90d1b876660e6b2e3e21
>
> Thanks for the quick reply,
> Enno
>
>
> On Mon, Jul 28, 2014 at 1:44 PM, Sebastien Besson <seb.besson at gmail.com>
> wrote:
>
>> Hi Enno,
>>
>> which version of Bio-Formats are you using? The upcoming 5.0.3 release of
>> Bio-Formats
>> will include a large set of bug fixes for the ND2 format.
>> Could you upload a sample file to
>> http://qa.openmicroscopy.org.uk/qa/upload/ for us to check
>> this release also addresses your issues?
>>
>> Best regards,
>> Sebastien
>>
>> On 28 Jul 2014, at 12:19, Enno R. Oldewurtel <
>> enno.oldewurtel at uni-koeln.de> wrote:
>>
>> Dear all,
>>
>> I just tried to read in ND2 files via matlab (either using r.openBytes
>> directly or bfopen.m). However, when specifying a sub-image with
>> x-origin>=2, the resulting image is skewed along a diagonal with slope
>> depending on the x-origin, i.e. slope=1 for x-origin=2. The y-origin works
>> with all values.
>>
>> This is the command I use:
>> test=bfopen(f,2,1,400,300);
>>
>> Using bfopen on a tif-file returns a correctly cropped image. Thus this
>> might be a nd2 specific problem.
>>
>> Has anyone experienced the same problem?
>>
>> These are images obtained with x-origin=1 and x-origin=2:
>> <x-originEquals1.png><x-originEquals2.png>
>>
>> Thanks,
>> Enno
>>
>>
>>
>> --
>> Enno R. Oldewurtel
>> AG Prof. B. Maier / Biophysics Group
>> Biozentrum
>> Universitaet zu Koeln
>> Zuelpicher Str. 47b
>> 50674 Koeln
>>
>> enno.oldewurtel at uni-koeln.de
>> http://www.biophysics.uni-koeln.de/
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>>
>
>
> --
> Enno R. Oldewurtel
> AG Prof. B. Maier / Biophysics Group
> Biozentrum
> Universitaet zu Koeln
> Zuelpicher Str. 47b
> 50674 Koeln
>
> enno.oldewurtel at uni-koeln.de
> Tel: +49-221-470-8048
> Fax: +49-221-470-6230
> http://www.biophysics.uni-koeln.de/
>
>
>


-- 
Enno R. Oldewurtel
AG Prof. B. Maier / Biophysics Group
Biozentrum
Universitaet zu Koeln
Zuelpicher Str. 47b
50674 Koeln

enno.oldewurtel at uni-koeln.de
Tel: +49-221-470-8048
Fax: +49-221-470-6230
http://www.biophysics.uni-koeln.de/
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