[ome-devel] Bio-Formats problem with AxioScan CZI files (uncompressed)

[Niko Ehrenfeuchter]

Dear all, dear Melissa,

we are required to deal with CZI data created by an Zeiss AxioScan.Z1 
SlideScanner:

* acquisition software is ZEN 2 (blue)
* tile-stitching was done directly after acquisition in "offline mode"
* results were saved as uncompressed CZI files

Trying to open them in Fiji using the latest Bio-Formats (5.1.8-DEV) 
works well for relatively small files (up to 12 GB tested) but fails for 
big files (100 GB tested).

The biggest working CZI consists of:
* 3 channels
* 9 z-slices
* 1 scene (Zeiss-speak for connected regions, i.e. tilings)

We tested other files containing more than one scene, they opened 
correctly as one image per scene.

The problematic 100 GB file consist of: 3ch, 3z, 8 scenes

Opening this file fails in the following way:

- Bio-Formats recognizes the CZI as an image sequence with 1008 images 
instead of 8 individual stitched images (one per scene).
- When opening one of the images in this sequence, the number of planes 
and channels are correct, but pixel values are all ZERO, i.e the entire 
image is black.
- The size of this image corresponds to the size of the full CZI, not 
the size of a scene, further reflecting that scenes are no more 
recognized as such.
- Metadata opens correctly and is attached to this mail (hoping the 
mailing list server lets the 7z compressed file pass).

According to our tests the critical parameter that leads to this 
behaviour seems to be purely the size of the CZI, as smaller files with 
a comparable complexity in structure are opened correctly.

To further put this into context, we wish to use OMERO to handle the 
massive amount of data that is created by the Slidescanner. From an 
experimenters perspective, the way this 100 GB data set was recorded is 
a realistic scenario.

We'd be very happy if you could help us in accomplishing this goal! 
Please let me know if there is a convenient way that we could make these 
datasets available to you.

Thanks and cheers,
Kai & Niko
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