CZI reader for loading input images

[sophiamaedler]

CZI reader has issues when files with multiple z-stacks are supplied.

[sophiamaedler]

Code snippet from @nordmannth using an alternative CZI reader package that seems more robust in use:

from aicsimageio import AICSImage

selected_czi = “path_to_.czi”

image = AICSImage(selected_czi)
print(“Dimensions:“, image.dims)
print(“Shape:“, image.shape)
print(“Number of scenes:“, image.scenes)

#if you have multiple scenes, best to choose one now (available scenes are given as output above)
image.set_scene(‘ScanRegion0’)

# filter as needed, for example:
scene1 = image.get_image_data(“CYX”)

# Rearrange the channels if necessary
scene1 = scene1[[0, 3, 1], :, :]

[sophiamaedler]

As a workaround until this solution is implemented users can use the above code snipped to load the czi file to memory and then pass it to the SPARCS project using project.load_input_from_array(scene1). If doing so please ensure that the dtype of the image is uint16 as this is what is expected by sparcspy.