| -verbose 3 | Verbosity of output. |
| -datatype u | Force writing of a new data type. |
| -sampling 1.5,1.5,1.5 | Sampling (A/pixel; a single value can be given). |
| -origin 0.8,-10,15.7 | Set the origin of the output image (default 0,0,0). |
| -size 1024,1024,120 | Output image size (default from tile file). |
| -mode 1 | Overlap handling: 0=average(default), 1=weigh, 2=central. |
| -rescale 127,27.5 | Rescale all input data to average and standard deviation. |
| -truncate -5,5.5 | Truncate data to minimum and maximum after rescaling. |
| -tiles text.tiles | Text file with overall size and tile origins. |
| -output output.img | Output image (default patch.pif). |
| -parameters file.star | Output micrograph parameter file. |