acryo 0.1.0

An extensible cryo-EM/ET toolkit for Python.

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 to make full use of CPU.
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.
5. Masked PCA clustering.

Install

pip install acryo -U