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https://github.com/brisvag/stemia
Scripts and Tools for Electron Microscopy Image Analysis.
https://github.com/brisvag/stemia
electron-microscopy python
Last synced: 19 days ago
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Scripts and Tools for Electron Microscopy Image Analysis.
- Host: GitHub
- URL: https://github.com/brisvag/stemia
- Owner: brisvag
- License: gpl-3.0
- Created: 2021-02-10T08:42:21.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2024-06-12T12:40:22.000Z (5 months ago)
- Last Synced: 2024-09-17T14:48:33.229Z (about 2 months ago)
- Topics: electron-microscopy, python
- Language: Python
- Homepage:
- Size: 216 KB
- Stars: 11
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# STEMIA
[](https://github.com/brisvag/stemia/raw/main/LICENSE)
[](https://pypi.org/project/stemia)
[](https://python.org)
**S**cripts and **T**ools for **E**lectron **M**icroscopy **I**mage **A**nalysis.
This is a simple personal collection of (sometimes...) useful scripts and tools for cryoem/cryoet.
## Installation
```bash
pip install stemia
```
You can quickly list all the available tools with
```
stemia -l
```
## Completion
You can enable completion for your bash shell by running:
```
eval "$(_STEMIA_COMPLETE=bash_source stemia)"
```
See [the click docs](https://click.palletsprojects.com/en/8.1.x/shell-completion/#enabling-completion) for how to do it for other shells.
## Tools
Everything is accessible through the main command line interface `stemia`.
Try `stemia -h` for help, or `stemia -l` for the command tree:
```
.stemia
├── aretomo: A collection of AreTomo-related tools and scripts.
│ ├── aln2xf: Convert AreTomo `aln` file to imod `xf` format.
│ └── batch: Run AreTomo on a full directory.
├── cryosparc: A collection of Cryosparc-related tools and scripts.
│ ├── csplot: Read a cryosparc job directory and plot interactively any column.
│ ├── fix_filament_ids: Replace cryosparc filament ids with small unique integers.
│ ├── generate_tilt_angles: Generate angle priors for a tilted dataset.
│ ├── merge_defects_gainref: Merge serialEM defects and gainref for cryosparc usage.
│ └── time_wasted: Print the total amount of time wasted on a project.
├── image: Simple image manipulation and processing.
│ ├── center_filament: Center an mrc image (stack) containing filament(s).
│ ├── classify_densities: Do hierarchical classification of particle stacks based on densities.
│ ├── create_mask: Create a mask for INPUT.
│ ├── extract_z_snapshots: Grab z slices at regular intervals from a tomogram as jpg images.
│ ├── flip_z: Flip the z axis for particles in a RELION star file.
│ ├── fourier_crop: Bin mrc images to the specified pixel size using fourier cropping.
│ ├── project_profiles: Project re-extracted and straightened membranes and get some stats.
│ │ ├── prepare: Generate and select 2D chunked projections for the input data.
│ │ ├── compute: Take the outputs from prepare and compute statistics and plots.
│ │ └── aggregate: Aggregate the generated data into general stats about given subsets.
│ └── rescale: Rescale an mrc image to the specified pixel size.
├── imod: A collection of IMOD-related tools and scripts.
│ └── find_NAD_params: Test a range of k and iteration values for nad_eed_3d.
├── relion: A collection of Relion-related tools and scripts.
│ ├── align_filament_particles: Fix filament PsiPriors so they are consistent within a filament.
│ └── edit_star: Simple search-replace utility for star files.
└── warp: A collection of Warp-related tools and scripts.
├── fix_mdoc: Fix mdoc files to point to the right data and follow warp format.
├── offset_angle: Offset tilt angles in warp xml files.
├── parse_xml: Parse a warp xml file and print its content.
├── prepare_isonet: Update an isonet starfile with preprocessing data from warp.
├── spoof_mdoc: Create dummy mdocs for warp.
├── summarize: Summarize the state of a Warp project.
└── preprocess_serialem: Prepare and unpack data from sterialEM for Warp.
```
### stemia aretomo aln2xf
```
Usage: stemia aretomo aln2xf [OPTIONS] ALN_FILE
Convert AreTomo `aln` file to imod `xf` format.
Options:
-f, --overwrite overwrite existing output
--help Show this message and exit.
```
### stemia aretomo batch
```
Usage: stemia aretomo batch [OPTIONS]
Run AreTomo on a full directory.
Options:
--help Show this message and exit.
```
### stemia cryosparc csplot
```
Usage: stemia cryosparc csplot [OPTIONS] JOB_DIR
Read a cryosparc job directory and plot interactively any column.
All the related data from parent jobs will also be loaded. An interactive
ipython shell will be opened with data loaded into a pandas dataframe.
JOB_DIR: a cryosparc job directory.
Options:
--drop-na drop rows that contain NaN values (e.g: micrographs with
no particles)
--no-particles do not read particles data
--no-micrographs do not read micrographs data
--help Show this message and exit.
```
### stemia cryosparc fix_filament_ids
```
Usage: stemia cryosparc fix_filament_ids [OPTIONS] STAR_FILE
Replace cryosparc filament ids with small unique integers.
Relion will fail with cryosparc IDs because of overflows.
Options:
-o, --star-output FILE where to put the updated version of the star file
[default: _fixed_id.star]
-f, --overwrite overwrite output if exists
--help Show this message and exit.
```
### stemia cryosparc generate_tilt_angles
```
Usage: stemia cryosparc 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: _tilted.star]
-f, --overwrite overwrite output if exists
--help Show this message and exit.
```
### stemia cryosparc merge_defects_gainref
```
Usage: stemia cryosparc merge_defects_gainref [OPTIONS] DEFECTS GAINREF
Merge serialEM defects and gainref for cryosparc usage.
requires active sbrgrid.
Options:
-d, --output-defects FILE
-o, --output-gainref FILE
-f, --overwrite overwrite output if exists
--help Show this message and exit.
```
### stemia cryosparc time_wasted
```
Usage: stemia cryosparc time_wasted [OPTIONS] [PROJECT_DIRS]...
Print the total amount of time wasted on a project.
Options:
-u, --useful_jobs TEXT ID of job that gave useful results. Its running time
and that of its parents will be used to calculate
useful time. Can be passed multiple times.
--help Show this message and exit.
```
### stemia image center_filament
```
Usage: stemia image 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.
```
### stemia image classify_densities
```
Usage: stemia image classify_densities [OPTIONS] [STACKS]...
Do hierarchical classification of particle stacks based on densities.
Options:
-c, --max-classes INTEGER
--help Show this message and exit.
```
### stemia image create_mask
```
Usage: stemia image create_mask [OPTIONS] INPUT OUTPUT
Create a mask for INPUT.
Axis order is zyx!
Options:
-t, --mask-type [sphere|cylinder|threshold]
-c, --center TEXT center of the mask (comma-separated floats)
-a, --axis INTEGER main symmetry axis (for cylinder)
-r, --radius FLOAT radius of the mask. If thresholding,
equivalent to "hard padding" [required]
-i, --inner-radius FLOAT inner radius of the mask (if any)
-p, --padding FLOAT smooth padding
--ang / --px whether the radius and padding are in
angstrom or pixels
--threshold FLOAT threshold for binarization of the input map
-f, --overwrite overwrite output if exists
--help Show this message and exit.
```
### stemia image extract_z_snapshots
```
Usage: stemia image extract_z_snapshots [OPTIONS] [INPUTS]...
Grab z slices at regular intervals from a tomogram as jpg images.
INPUTS: any number of paths of volume images
Options:
-o, --output-dir PATH
--mrc also output mrc files
-n, --n-slices INTEGER number of equidistant slices to extract
--keep-extrema whether to keep slices at z=0 and z=-1 (if false,
slices is reduced by 2)
-a, --average INTEGER number of slices to average over
-s, --size TEXT size of final image (X,Y)
-r, --range TEXT range of slices to image (A,B)
--axis INTEGER axis along which to do the slicing
--help Show this message and exit.
```
### stemia image flip_z
```
Usage: stemia image 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.
```
### stemia image fourier_crop
```
Usage: stemia image fourier_crop [OPTIONS] [INPUTS]...
Bin mrc images to the specified pixel size using fourier cropping.
Options:
-b, --binning FLOAT binning amount [required]
-f, --overwrite overwrite output if exists
--help Show this message and exit.
```
### stemia image project_profiles prepare
```
Usage: stemia image project_profiles prepare [OPTIONS] [PATHS]...
Generate and select 2D chunked projections for the input data.
Options:
-o, --output PATH [required]
-s, --chunk-size INTEGER
-f, --overwrite
--help Show this message and exit.
```
### stemia image project_profiles compute
```
Usage: stemia image project_profiles compute [OPTIONS] PROJ_DIR
Take the outputs from prepare and compute statistics and plots.
Options:
-f, --overwrite
--help Show this message and exit.
```
### stemia image project_profiles aggregate
```
Usage: stemia image project_profiles aggregate [OPTIONS] [INPUTS]...
Aggregate the generated data into general stats about given subsets.
Inputs are subdirectories of the project_dir from compute.
Options:
-o, --output-name TEXT Title/filename given to the aggregated outputs.
--help Show this message and exit.
```
### stemia image rescale
```
Usage: stemia image 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.
```
### stemia imod find_NAD_params
```
Usage: stemia imod find_NAD_params [OPTIONS] INPUT
Test a range of k and iteration values for nad_eed_3d.
Options:
-k, --k-values TEXT
-i, --iterations TEXT
-s, --std TEXT
--help Show this message and exit.
```
### stemia relion align_filament_particles
```
Usage: stemia relion align_filament_particles [OPTIONS] STAR_FILE
Fix filament PsiPriors so they are consistent within a filament.
Read a Relion STAR_FILE with in-plane angles and filament info and flip any
particle that's not consistent with the rest of the filament.
If a consensus cannot be reached, or the filament has too few particles,
discard the whole filament.
Options:
-o, --star-output FILE where to put the updated version of the star
file [default: _aligned.star]
-t, --tolerance FLOAT angle in degrees within which neighbouring
particles are considered aligned
-c, --consensus-threshold FLOAT
require an angle consensus at least higher
than this to use a filament.
-d, --drop-below INTEGER drop filaments if they have fewer than this
number of particles
-r, --rotate-bad-particles rotate bad particles to match the rest of
the filament
-f, --overwrite overwrite output if exists
--help Show this message and exit.
```
### stemia relion edit_star
```
Usage: stemia relion edit_star [OPTIONS] [STAR_FILES]...
Simple search-replace utility for star files.
Full regex functionality works (e.g: reusing groups in output)
Options:
-s, --suffix-output TEXT suffix added to the output files before extension
-c, --column TEXT column(s) to modify
-i, --regex-in TEXT regex sed-like search pattern(s)
-o, --regex-out TEXT regex sed-like substitution to apply to the
column(s)
-f, --overwrite overwrite output if exists
--help Show this message and exit.
```
### stemia warp fix_mdoc
```
Usage: stemia warp fix_mdoc [OPTIONS] MDOC_DIR
Fix mdoc files to point to the right data and follow warp format.
Options:
-d, --data-dir PATH
--dates fix date format
--paths fix image paths
--help Show this message and exit.
```
### stemia warp offset_angle
```
Usage: stemia warp offset_angle [OPTIONS] [WARP_DIR]
Offset tilt angles in warp xml files.
Options:
--help Show this message and exit.
```
### stemia warp parse_xml
```
Usage: stemia warp parse_xml [OPTIONS] XML_FILE
Parse a warp xml file and print its content.
Options:
--help Show this message and exit.
```
### stemia warp prepare_isonet
```
Usage: stemia warp prepare_isonet [OPTIONS] WARP_DIR ISO_STAR
Update an isonet starfile with preprocessing data from warp.
Options:
--help Show this message and exit.
```
### stemia warp spoof_mdoc
```
Usage: stemia warp spoof_mdoc [OPTIONS] [RAWTLT_FILES]...
Create dummy mdocs for warp.
RAWTLT_FILES: simple file with one tilt angle per line. Order should match
sorted filenames.
Options:
-d, --dose-per-image FLOAT electron dose per tilt image (or per frame if
inputs are movies) [required]
-p, --pixel-size FLOAT
-e, --extension [tif|mrc]
-f, --overwrite
--help Show this message and exit.
```
### stemia warp summarize
```
Usage: stemia warp summarize [OPTIONS] [WARP_DIR]
Summarize the state of a Warp project.
Reports for each tilt series: - discarded: number of discarded tilts -
total: total number oftilts in raw data - stacked: number of image slices in
imod output directory - mismatch: whether stacked != (total - discarded) -
resolution: estimated resolution if processed
Options:
--help Show this message and exit.
```
### stemia warp preprocess_serialem
```
Usage: stemia warp preprocess_serialem [OPTIONS] RAW_DATA_DIR
Prepare and unpack data from sterialEM for Warp.
You must be in a new directory for this to work; new files will be placed
there with the same name as the original tifs.
RAW_DATA_DIR: the directory containing the raw data
Options:
--help Show this message and exit.
```