Support Zeiss CZI format

Wei Chen chenw1 at uthscsa.edu
Fri Oct 7 12:17:34 EDT 2022


Hi,

I am working on Zeiss CZI driver.

https://github.com/venklab/openslide/tree/axioscan7

It reads bright field CZI file in JPEG XR and uncompressed format.
The microscope is AxioScan7. I can only make it generates these two
formats. Cannot find an option to produce JPEG or LZW or ZSTD CZI
therefor these decoders are not included in the driver.

It works for slide with single or multiple sections, or scenes, in CZI's
term. Slide label is also recognized and available in associated images.

AxioScan7 is able to capture multiple channels, such as multiple
grayscale channels for fluorescence. Its default is 14bits grayscale. I
need test downscale them to 8bits then remix grayscale channels into
single ARGB.

The JPEG XR decoder is from jxrlib, which is included in CentOS, Debian
and Ubuntu. Because CentOS7, Debian 10 and 11, Ubuntu < 22 are all
missing pkg-config file, an autogen.sh script is included to generate
libjxr.pc for configure.

I will send pull request after more testing.


Best,
Wei


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