Scripts and Tools for Electron Microscopy Analysis.
Project description
STEMIA
Scripts and Tools for Electron Microscopy Image Analysis.
This is a simple personal collection of (sometimes...) useful scripts and tools for cryoem/cryoet.
Installation
pip install stemia
Tools
Everything is accessible through the main command line interface stemia
. Try stemia -h
.
aretomo_align
Usage: stemia aretomo_align [OPTIONS] [WARP_DIR]
run aretomo on a warp directory (after imod stacks were generated).
Requires ccderaser and AreTomo.
Assumes the default Warp directory structure with generated imod stacks
Options:
-d, --dry-run only print some info, without running the
commands
-t, --tilt-axis FLOAT starting tilt axis for AreTomo, if any
-f, --overwrite overwrite any previous existing run
--fix / --nofix run ccderaser to fix the stack
--norm / --nonorm use mrcfile to normalize the images
--align / --noalign run aretomo to produce an alignment
--startfrom [raw|fix|norm] use outputs from a previous run starting from
this step
--ccderaser TEXT command for ccderaser
--aretomo TEXT command for aretomo
--help Show this message and exit.
center_filament
Usage: stemia center_filament [OPTIONS] INPUT [OUTPUT]
Center an mrc image containing filament(s). Can update particles in a
RELION .star file accordingly.
If OUTPUT is not given, default to INPUT_centered.mrc
Options:
-s, --update-star FILE a RELION .star file to update with new
particle positions
-o, --star-output FILE where to put the updated version of the star
file. Only used if -s is passed [default:
STARFILE_centered.star]
--update-by [class|particle] whether to update particle positions by
classes or 1 by 1. Only used if -s is passed
[default: class]
-f, --overwrite overwrite output if exists
-n, --n-filaments INTEGER number of filaments on the image [default: 2]
-p, --percentile INTEGER percentile for binarisation [default: 85]
--help Show this message and exit.
csplot
Usage: stemia csplot [OPTIONS] [CS_FILE]...
read a cryosparc file (plus any number of passthrough files) into a pandas
dataframe and provide a simple interface for plotting columns. Provided
files must be compatible (have the same uid column!)
Options:
--help Show this message and exit.
flip_z
Usage: stemia flip_z [OPTIONS] STAR_PATH
STAR_PATH: star file to flip along z assume all micrographs have the same
shape
Options:
-o, --output FILE
-m, --mrc_path FILE
--star_pixel_size FLOAT
--mrc_pixel_size FLOAT
--z_shape INTEGER
--help Show this message and exit.
generate_tilt_angles
Usage: stemia generate_tilt_angles [OPTIONS] STAR_FILE TILT_ANGLE TILT_AXIS
Read a Relion STAR_FILE with in-plane angles and generate priors for rot
and tilt angles based on a TILT_ANGLE around a TILT_AXIS.
Options:
-r, --radians Provide angles in radians instead of degrees
-o, --star-output FILE where to put the updated version of the star file
[default: <STAR_FILE>_tilted.star]
-f, --overwrite overwrite output if exists
--help Show this message and exit.
rescale
Usage: stemia rescale [OPTIONS] INPUT OUTPUT TARGET_PIXEL_SIZE
Rescale an mrc image to the specified pixel size.
TARGET_PIXEL_SIZE: target pixel size in Angstrom
Options:
--input-pixel-size FLOAT force input pizel size and ignore mrc header
-f, --overwrite overwrite output if exists
--help Show this message and exit.
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