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

[Sebastian Rhode]

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
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