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

[Enno R. Oldewurtel]

Hi Sebastien,
is it possible to not only crop, but also downsample when reading an nd2
file? Using the PixelRegion Parameter when reading in tif files via
matlab's imread function, one can also specify an increment. This is useful
for me when I quickly want to display a very large image for overview,
where it is sufficient to only see every 5th pixel or so.

On another note, the 5.0.2-DEV version is more than a factor of two faster
executing r.setID for nd2 files on my system, which is very much
appreciated by me!

Thanks,
Enno



On Mon, Jul 28, 2014 at 2:52 PM, Enno R. Oldewurtel <
enno.oldewurtel at uni-koeln.de> wrote:

> 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/
>



-- 
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/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20140729/2e192a29/attachment.html>