Implementation of a CZI (Zeiss) driver

[BALBASTRE Yael 237482 Thésard]

Hi,

Since our lab has acquired a Zeiss Axio-Scan scanner, we are interested in adding a czi reader to OpenSlide (that we are already using to read other WSI images). We already had a few contacts with Benjamin Gilbert, but it must be better to ask my questions using this mailing list.

The CZI format has been entirely specified by Zeiss and, contrary to most formats present in OpenSlide, does not use a tiff base, even though the principles are shared. A file contains several subblocks, each containing a subimage which can be compressed (jpeg or jpegXR mainly) or not, as well as metadata stored in the file as xml blocks.

To follow up the question I asked to Mr Gilbert regarding the file supposed to host czi-related code, I am not comfortable with having all of it in a single openslide-zeiss-vendor.c source, especially since it would deal both with file stream reading (decoding of the hard directories/subblocks/attachments structure) and with more high-level, microscopy-related treatment (metadata, grid-building, subimages decoding...).
I would rather have the stream reading separated and placed in a different source file along with a clear API (which would resemble the tiff decoder). I understand that it is different from what has been done before, but maybe the issue had never been on the table because none of the previous formats had such a specification ? (the only one I see coming close is MIRAX).
If you still prefer to have everything in one big source, I will obviously go this way.

Thanks a lot for your time.

Best regards,
Yaël Balbastre

Yaël Balbastre - PhD student
CEA/DSV/I²BM/MIRCen/LMN
Image Processing Team - bioPICSEL
18 route du Panorama - BP6
92265 FONTENAY-AUX-ROSES CEDEX
FRANCE
T 33 (1) 46 54 92 83
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