[ome-users] BioFormats Import does not uses correct order for Multi-Series CZI files

[Emil Rozbicki]

Hi Sebastian,

That's great, thank you very much. I have created a ticket for that issue and CC'd you on it.
https://trac.openmicroscopy.org.uk/ome/ticket/12673

Regards,
Emil


On 1 Dec 2014, at 08:45, Sebastian Rhode <sebrhode at gmail.com> wrote:

> Hi Emil,
> 
> done. I uploaded the file. Di not hesitate to contact me for info since I am really interested in solving this issue ...
> 
> Sebi
> 
> 2014-11-28 16:08 GMT+01:00 Emil Rozbicki <emil at glencoesoftware.com>:
> Hi Sebastian,
> 
> I gave you a wrong link, sorry. Could you try this one: https://www.openmicroscopy.org/qa2/qa/upload/
> 
> Cheers,
> Emil
> 
> 
> On 28 Nov 2014, at 14:03, Sebastian Rhode <sebrhode at gmail.com> wrote:
> 
>> Hi Emil,
>> 
>> i tried, but got an upload error...
>> 
>> Sebi
>> 
>> <image.png>
>> 
>> 2014-11-28 11:29 GMT+01:00 Emil Rozbicki <emil at glencoesoftware.com>:
>> Hi Sebastian,
>> 
>> Thanks for reporting the issue. Would you mind uploading some example files that show this problem to our QA system http://qa.openmicroscopy.org.uk/.
>> 
>> Regards,
>> Emil
>> 
>> 
>> On 27 Nov 2014, at 10:57, Sebastian Rhode <sebrhode at gmail.com> wrote:
>> 
>>> Hi,
>>> 
>>> when I acquire a CZI within the ZEN software with 2 Scences, where every Scene by itself is a 2x1 Tile, the image looks like this: --> see 2 screenshots from ZEN for Scene 1 and 2.
>>> 
>>> There the "Acquistion order" is clear. I used the OME-Testimages with a TestCam Feature to make the images recognizable.
>>> 
>>> The problem is, that the BioFormtas CZIReader does no distinct dimension for Scenes and Tiles.
>>> In ZEN inside the CZI file there is an S-Index (Scence) and M-Index(Tile).
>>> 
>>> The order of acquistion for the example is
>>> 
>>> S=0 M=0 --> Image 1
>>> S=0 M=1 --> Image 2
>>> S=1 M=0 --> Image 3
>>> S=1 M=1 --> Image 4
>>> 
>>> But the CZIReader seems to use the M-Index as its outer loop index and the result is:
>>> 
>>> S=0 M=0 --> Image 1
>>> S=1 M=0 --> Image 3
>>> S=0 M=1 --> Image 2
>>> S=0 M=1 --> Image 4
>>> 
>>> This makes is quite hard to import CZI data from for instance well images, where every well corresponds to a scence. When one uses a Tile inside a well, the BioFormat import mixes up the images and assigns images to wells, where they where not acquired.
>>> 
>>> Is it possible to modify the CZIReader in an way that it reads the Image Series correctly in the order of acquisition?
>>> 
>>> Cheers,
>>> 
>>> Sebi
>>> 
>>> <CZI_Order_Test_Scene=2_Tile=2x1.czi><Scene_Image_Import_BioFormats_Problem.png><ZEN_Scene1.png><ZEN_Scene2.png>_______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>> 
>> 
>> 
>> 
>> -- 
>> Dr. Sebastian Rhode
>> Grünwalder Straße 103a
>> 81547 München
>> Tel: +49 89 4703091
>> Mobil: +49 151 40767993
>> sebrhode at gmail.com
> 
> 
> 
> 
> -- 
> Dr. Sebastian Rhode
> Grünwalder Straße 103a
> 81547 München
> Tel: +49 89 4703091
> Mobil: +49 151 40767993
> sebrhode at gmail.com

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