Metadata-Version: 2.1
Name: acryo
Version: 0.0.5
Summary: An extensible cryo-EM/ET toolkit for Python.
Author: Hanjin Liu
Author-email: liuhanjin-sc@g.ecc.u-tokyo.ac.jp
License: BSD 3-Clause
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy (>=1.21)
Requires-Dist: scipy (>=1.7.3)
Requires-Dist: pandas (>=1.3)
Requires-Dist: dask (>=2021.6.0)
Requires-Dist: typing-extensions (>=4.1.1)

# acryo

An extensible cryo-EM/ET toolkit for Python. Currently only the subtomogram averaging part is implemented.
The purpose of this library is to make data analysis on cryo-EM/ET more available for scientists.

### Highlights

1. Out-of-core and parallel processing by `SubtomogramLoader`. It uses
   [dask](https://github.com/dask/dask) to make full use of CPU.
   ![](images/task-graph.png)
2. Alignment algorithms are highly extensible by inheriting `BaseAlignmentModel` for the most
   low-level implementation or `TomographyInput` for extension at more practical-level. You
   can customize pre-processing, alignment function and easily extend it to support multi-
   reference alignment.
3. Concise representation of subtomograms, using `numpy.ndarray` for positions and
   `scipy.spatial.transform.Rotation` for orientation.
4. Tomogram simulation using `TomogramSimulator`.

### Contribution

Contribution is very welcome!
