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 in batch on data preprocessed in warp.
Needs to be ran after imod stacks were generated. Requires ccderaser and
AreTomo. Assumes the default Warp directory structure with generated imod
stacks. Some warp xml files may be updated to disable too dark images.
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 (stack) 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 cryosparc file(s) and plot interactively any column.
An interactive ipython shell will be opened with data loaded into a pandas
dataframe.
CS_FILE: a .cs file followed by any number of passthrough files
Options:
--help Show this message and exit.
flip_z
Usage: stemia flip_z [OPTIONS] STAR_PATH
Flip the z axis for particles in a RELION star file.
STAR_PATH: star file to flip along z
Assumes all tomograms 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
Generate angle priors for a tilted dataset.
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.
parse_warp_xml
Usage: stemia parse_warp_xml [OPTIONS] XML_FILE
Parse a warp xml file and print its content.
Options:
--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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