cryospax 0.1.1

A small library for cryo-EM single particle analysis in JAX.

Single particle analysis tools for cryoJAX

CryoSPAX is a small library built to support cryoJAX projects that implement single-particle analysis (SPA) at scale. It seeks to simplify new cryo-EM research, rather than providing end-to-end single particle analysis workflows.

Installation

If you are not installing JAX with GPU or TPU support, installing cryospax in a fresh uv environment is as simple as

uv venv --python=3.11 ~/path/to/venv/
source ~/path/to/venv/bin/activate
uv pip install cryospax

If you are installing JAX with GPU or TPU support, first follow the JAX installation instructions. It may also be necessary to directly follow the cryojax installation instructions for installs with advanced cryoJAX features.

To install cryospax in development mode, run

git clone https://github.com/michael-0brien/cryospax
cd cryospax
git checkout dev
uv pip install -e '.[dev,tests]'
uv run pre-commit install

Acknowledgements

• CryoSPAX is made possible by the teamtomo ecosystem for open source cryo-EM software (e.g. starfile).