| -verbose 7 | Verbosity of output. |
| -consolidate | Only consolidate particles based on distance. |
| -locdiff | Calculate the difference in the locations. |
| -fomdiff | Calculate the difference in the foms. |
| -printlocdiff | Print the difference in the locations. |
| -printanglediff | Print the difference in the view angle. |
| -printalphadiff | Print the difference in the alpha angles. |
| -thrlocdiff 10.0 | Analyse only particles below threshold (pixels). |
| -thranglediff 20.0 | Analyse only particles below threshold (degrees). |
| -remove | Remove all particles with selection number 0. |
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