importing tiff stack for target space

[shermas]

Hey,

I am unable to use my 3D imaging data when assigning locations.
I kept on getting the following errors: “IndexError: too many indices for array: array is 2-dimensional, but 3 were indexed “
After running the command: “locations_from_image = novosparc.gm.create_target_space_from_image(tissue_path)”
The tissue path leads to a binarized .tif 3D expression image.

I ended changing the function in the following way:

tissue_path = '/…/_template_binarized_inverted.tif'
img = io.imread(tissue_path)
img_width = img.shape[2]
img_height = img.shape[1]
img_depth = img.shape[0]

locations = np.array([(x, y, z) for x in range(img_width) for y in range(img_height) for z in range(img_depth)
if sum(img[z, y, x, :] == np.array([0, 0, 0]))])

It would be good if this could be implemented in novosparc.

Best,
Shachar