usage: A simple template matching script. run [prog] <tomogram> <reference> to extract particles from tomogram. Results will be saved in the corresponding info files and can be visualized via spt_boxer

Option Type Description
--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