| -all | Select all markers. |
| -updatematrix | Update micrograph matrices from tilt and axis angles. |
| -lambda 2650 | Calculate thickness from proportionality coefficient (in angstrom). |
| -adjusttilt | Apply tilt adjustments based on intensity variation. |
| -pick 1,20,1 | Pick seed markers in reference image (1) or all images (2), |
| excluding the distance from the edge (in pixels). |
| and a flag to add to rather than replace existing markers. |
| -generatemarkers | Generates markers for all micrographs from a seed. |
| -findaxis 10,1.5,-30,50 | Finds the tilt axis using seed markers and micrographs |
| near the given tilt angle and with the axis angle step size, |
| start and end (default axis parameters: 1,-180,180). |
| -track 5,1.5 | Track markers: number of iterations and residual target (default 10% of marker radius). |
| using zero-tilt reference markers as seed. |
| -crossmarker | Cross-correlate markers during z-search (default real space correlate). |
| -recenter | Recenter z coordinates during tracking (default not). |
| -refine shifts | Refine marker parameters: |
| markers: Refine marker micrograph positions. |
| z: Refine marker z positions. |
| origins: Refine micrograph origins. |
| scales: Refine micrograph scales. |
| views: Refine view transforms. |
| all: Refine origins, scales and views simultaneously. |
| 8,v,o,z: Refine iteratively in sequence views, origins and z's. |
| -resetmodel | Reset the x and y marker coordinates to that of the zero-degree tilt image. |
| -angles | Calculate micrograph orientation angles. |
| -check | Determine if markers all fall within micrograph boundaries. |
| -fix | Fix markers falling outside micrograph boundaries. |
| -errors 1.6 | Show errors above this threshold (distance in pixels). |
| -exclude 0,1,134-140 | Exclude these micrographs (can be "none"). |
| -deselect 5-9,33 | Deselect markers by id from all micrographs and models. |
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