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
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 inw1_maskandw2_mask.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_maskandw2_maskto be 8-bit unsigned integers instead and that solved the problem albeit the images are lower resolution.Python version:
Python 3.13.1