Scikit-Image imsave outputs black images

[daancs]

Hi!

I am using the same setup as in Issue #1.

In the SegmentationPart1 class, in the run_single() function the following lines output completely black images regardless of values in w1_mask and w2_mask.

w1_mask = np.uint16(w1_mask)
w2_mask = np.uint16(w2_mask)
sio.imsave(self.save_path / set_mask_save_name(well_id, fov, 0), w1_mask, check_contrast=False)
sio.imsave(self.save_path / set_mask_save_name(well_id, fov, 1), w2_mask, check_contrast=False)

This could be due to scikit-images imsave function cannot save unsigned 16-bit integer arrays into files (probably deprecated?), see stackoverflow here.

I changed the w1_mask and w2_mask to be 8-bit unsigned integers instead and that solved the problem albeit the images are lower resolution.

Python version: Python 3.13.1