li'l AreTomo

A lightweight Python API for AreTomo.

Installation

It is recommended to install into a fresh virtual environment.

pip install lil_aretomo

Usage

import numpy as np
import mrcfile
from lil_aretomo import align_tilt_series

tilt_series = mrcfile.read('my_tilt_series.mrc')

align_tilt_series(
    tilt_series=tilt_series,
    tilt_angles=np.linspace(-60, 60, 41),
    pixel_size=1.35,  # angstroms per pixel
    sample_thickness_nanometers=2000,  # angstroms
    correct_tilt_angle_offset=True,
    basename='TS_01',  # basename for files passed to AreTomo
    output_directory='TS_01_AreTomo',
    skip_if_completed=False, # set to True to skip if results from a previous alignment are present
    executable='AreTomo' # command to run AreTomo
)

For developers

We use pre-commit to ensure code style and formatting remains consistent.

To install the package in editable mode development dependencies

pip install -e .[dev]
pre-commit install

Flake8, black and isort will then run automatically on each commit.