| --version |
None |
show program's version number and exit |
| --reference |
None |
Specify a 3D reference volume. This should be 'light contrast', ie - positive isosurface. |
| --label |
str |
Assign unique label to particles resembling specified reference. This allows specific particles to be extracted in the next step and aids project organization with easily interpreted filenames.\nIf --label is not specified, this set of particles will be labeled according to the file name of the reference without file extension. |
| --nptcl |
int |
maximum number of particles per tomogram |
| --dthr |
float |
The program will remove particles closer than this distance threshold. By default, this will be 1/2 of box size or the reference. Otherwise, specify the distance in Angstrom. |
| --vthr |
float |
template matching value threshold (n sigma). Particles with score lower than this will be removed. |
| --delta |
float |
Anglular sampling to rotate the reference. |
| --sym |
str |
Symmetry of reference. |
| --rmedge |
None |
Remove particles on the edge. |
| --rmgold |
None |
Remove particles near gold fiducial. |
| --boxsz |
int |
Overwrite box size of the reference. This should be the box size of unbinned micrographs if specified. |
| --threads |
int |
number of threads to use |
| --shrink |
int |
binning factor. Default (-1) will downsample the tomograms to ~500px for template matching |
| --ppid |
int |
ppid |