-s
The primary signal channel: test_brain/ch00
-b
The secondary autofluorescence channel (or background): test_brain/ch01
-o
The output directory : test_brain/output
--orientation
The data orientation: psl
-v
The voxel spacing in the same order as the data orientation (psl
): 5 2 2
--atlas
The atlas we want to use: allen_mouse_10um
allen_mouse_25um
atlas either way, as registration with the high-resolution atlas requires about 30GB for this image.2020-10-14 00:07:20 AM - INFO - MainProcess main.py:86 - Finished. Total time taken: 3:22:42
--start-plane 1500 --end-plane 1550
--atlas allen_mouse_25um
allen_mouse_25um
atlas either way, as registration with the high-resolution atlas requires about 30GB for this image.