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

[Emil Rozbicki]

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>_______________________________________________
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