Thanks for all responding.
I've solved this problem. It simply need to turn on the debug mode at the beginning of the script. In my case, I turned on the change the code to 'ws.debug = True' in the Initialize workspace cell.
Encountering an error when running this cell, does any one know how to fix it? Thank you.
cfos and autofluo images have been resampled align with the template/reference file in atlas. Is it necessary to debug this file?
File "/homeanaconda3/envs/ClearMapStable/lib/python3.6/site-packages/tifffile/tifffile.py", line 4696, in open
self._fh = open(self._file, self._mode)
FileNotFoundError: [Errno 2] No such file or directory: '/home/ClearMap2/Documentation/Example/Haloperidol/haloperidol/1268/debug_resampled.tif'
ClearMap2 - Cell alignment section - file not found error