| -invert | Invert density in the image. |
| -rescale -0.1,5.2 | Rescale data to average and standard deviation after filtering. |
| -dose 2.5 | Weigh the amplitudes by accumulated dose using the given dose/frame (e/Å2). |
| -normalize 2 | Normalize amplitudes (1:amplitude; 2:power). |
| -root | Weigh by the square root of the amplitudes. |
| -square | Weigh by the squares of the amplitudes. |
| -verbose 7 | Verbosity of output. |
| -datatype u | Force writing of a new data type. |
| -sampling 1.5,1.5,1.5 | Sampling (A/pixel; default from input file; a single value can be given). |
| -resolution 15 | Resolution limit (angstrom) |
| -RPS file.txt | Radial power spectrum. |
| -FSC file.xml | FSC curve. |
| -Reference file.map | Reference map. |
| -Mask mask.tif | Mask file to exclude regions in reciprocal space. |
| -mask mask.mrc | Real space mask to apply before weighing. |