Particle Stack

usage: particle_stack [-h] [--image-root IMAGE_ROOT] [-o OUTPUT] [--size SIZE]
                      [--threshold THRESHOLD] [--resize RESIZE]
                      [--image-ext IMAGE_EXT] [--metadata METADATA]
                      file

Positional Arguments

file

path to input coordinates file

Named Arguments

--image-root

root directory of the micrograph files

-o, --output

path to write particle stack file

--size

size of particle stack images

--threshold

only take particles with scores >= this value (default: -inf)

Default: -inf

--resize

rescaled particle stack size. downsamples particle images from size to resize pixels. (default: off)

Default: -1

--image-ext

image file extension (default=.mrc)

Default: “.mrc”

--metadata

path to .star file containing per-micrograph metadata, e.g. CTF parameters (optional)