| -invert | Invert mask before other operations. |
| -dilate 2 | Dilate mask a number of times. |
| -switch 3,6 | Switch two levels. |
| -color size | Generate a RGBA image (random/level/size). |
| -size | Convert level mask to region size map. |
| -level 134 | Convert a mask to multiple levels, with the given voxels per level. |
| -bands 250,-1,150,1,30,0 | Banded mask for reciprocal space (pairs of numbers: angstrom,value). |
| Band with 0: Not used. |
| Band with 1: Use for orientation determination. |
| Band with -1: Use for cross-validation. |
| -collapse | Convert a multi-level mask to a binary mask. |
| -interfaces 3 | Calculates interfaces for the indicated region (-1 gives whole matrix). |
| -merge 25,4 | Calculates a region interface matrix and deletes/merges |
| regions smaller than the given size and interface size. |
| -symmetry C5 | Set all symmetry-related segments to the same index. |
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