| -scale 1.56 | Isotropic scale (required to resize the data). |
| -translate 0.3,-4.1,3.3 | Translation. |
| -bandpass 25.3,200 | Bandpass filter: resolution limits (angstrom). |
| -filterextremes | Remove extreme regions (such as micrograph labels) |
| -verbose 7 | Verbosity of output |
| -datatype u | Force writing of a new data type |
| -origin 0,-10,30 | Set origin, used with -size option (default 0,0,0) |
| -size 22,33,14 | New size (voxels, default from data) |
| -sampling 2,3.5,1 | Sampling before rescaling (angstrom/voxel, a single value sets all three) |
| -reference ref.map | Reference for resizing. |