This script browses through the slices inside a .czi file coming from the Slide Scanner, allows the user to select the final resolution and channels, and saves one image per slice.
It depends on functions that are located in the following repo, so make sure you have them in your Fiji:
https://github.com/HernandoMV/czi-rs-functions
Drag "czi_extract_slices.py" (inside "czi_extract_slices" folder) to Fiji, modify the header to the desired parameteres, and run it.
It is used in larger pipelines like this one TODO: insert here link to PH3 analysis repo