| -reconstructions | Operate on reconstruction parameters rather than micrographs. |
| -add | Add micrograph coordinates and particle origins (default not). |
| -find 120,130 | Find particles using a ring within these radii (voxels). |
| -extract 150,110,120 | Extract particles with these radii (voxels, one sets all). |
| -background | Correct background of extracted particles. |
| -normalize | Normalize extracted particles. |
| -center 23.5,200 | Center each particle image before extraction, using these resolution limits. |
| -verbose 7 | Verbosity of output. |
| -sampling 1.5,1.5,1.5 | Sampling (A/pixel; a single value can be given). |
| -fill 127 | Fill value for particles extending beyond image (default background). |
| -base subvol | Set the particle base file name (no extension). |
| -path dir/subdir | Set the particle file paths. |
| -extension pif | Set the particle image file format. |
| -output file.star | Output parameter file. |