[Feature] Use .CZI data in SOPA

[mariavigovaldoleiros]

Feature request I am using multiplexed images (Opal dyes - fluorescence data) acquired with a Zeiss microscope that generates .czi files, but this format is not compatible with SOPA.

Suggested solution Update PhenoCycler technology to accept .czi data as raw inputs.

Alternative Create a technology (e.g. ‘Opal System’) that accepts .czi as raw input.

Thank you!

[quentinblampey]

Hello @mariavigovaldoleiros, thanks for creating this issue, you're actually not the first one to ask for a .czi file reader. I'll work on this and come back to you very soon!

[quentinblampey]

This is available in sopa==1.0.11, via a new reader called aicsimageio. It uses AICSImageIO, which supports reading multiple formats, including CZI. Note that, as the docs mentions, you'll need to pip install aicsimageio and pip install aicspylibczi.

The usage is the same as the other readers, and the path argument refers to one CZI file.

Let me know how it goes!

[quentinblampey]

I'm closing this issue, but feel free to re-open if you need extra information!