| -add | Add input images after transforming the second. |
| -filterextremes | Filter micrograph extremes before aligning. |
| -verbose 7 | 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). |
| -tile 1024,1024,5 | Size of tiles for correlation (default 512,512,1). |
| -resolution 30,500 | High and low resolution limits for cross-correlation (default 0.1,1000). |
| -maxshift 55 | Maximum allowed shift (default 1/4 of tile). |