Convert CZI to TIFFs for CD7 screens

czi_to_tiffs.py

import os
import tifffile as tiff
from bioio import BioImage

img = BioImage("E:/240416_NA_1-unprocessed-202404171807.czi")
destination = "E:/temp/"

if not os.path.exists(destination):
    os.makedirs(destination)

for scene_id, scene in enumerate(img.scenes):
    img.set_scene(scene)
    
    for time_point in range(img.dims.T):
        for z_slice in range(img.dims.Z):
            for channel in range(img.dims.C):
                filename = destination + f"Image-03_H(0)_S{scene_id:04d}({scene})_T{time_point:06d}_Z{z_slice:04d}_C{channel:02d}_M0000_ORG.tif"
                tiff.imwrite(filename, img.get_image_data("YX", T=time_point, Z=z_slice, C=channel))