| -all | Select all markers. |
| -updatematrix | Update micrograph matrices from tilt and axis angles. |
| -resetmodel | Reset the x and y coordinates to that of the zero-degree tilt image. |
| -checkmarkers | Determine if markers all fall within micrograph boundaries. |
| -deselect 5-9,33 | Deselect markers by id from all micrographs and models. |
| -deletemarkers 5-9,33 | Delete markers by id from all micrographs and models. |
| -rotationaxis | Determine the best rotation axis from refined markers. |
| -clear 240,7.5 | Clear extraneous areas on micrographs with this intended reconstruction thickness |
| and smoothing edge width (default 5). |
| -removemarkers 14 | Mask out markers with this radius (pixels) before transformation. |
| -thickness 234 | Calculate mean free path from a given thickness (in angstrom). |
| -lambda 2650 | Calculate thickness from proportionality coefficient (in angstrom). |
| -catenate | Concatenate separate micrograph image files into one file. |
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