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

[Sebastien Besson]

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/

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