voxelium-apex 0.1.0

Voxelium-apex: a package for cryoEM/cryoET heterogeneity reconstruction analysis and visualization

Voxelium-apex

This repository contains the voxelium-apex codes -- a package for cryoEM/cryoET heterogeneity reconstruction analysis and visualization.

Installation

Install from PyPI

First create and activate a Conda or standard Python virtual environment. Then install the prebuilt wheels distributed via PyPI: pip install voxelium-apex

Build from source

After cloning the repository and navigating (cd) into the project directory, first create and activate a Conda or standard Python virtual environment. pip install .

3D Spectral Heterogeneity Analysis (SHA)

Run vxm-apex -h to see a list of modules. To run the analysis, the sha3D module can be run as follows:

vxm-apex sha3d <input_star_data> <log_directory> --gpu 0

Here, <input_star_data> is an input STAR-file containing all the particles with CTF and pose parameters set. <log_directory> will contain the results of the job.

NOTE: Adding --preload speeds things up considerably, assuming the dataset fits in memory.

NOTE: You need to install extension for this, see above.

SHA3D Visualization

To visualize the results run:

vxm-apex sha3d_viewer <log_directory>

In the above, <log_directory> is the path to the directory containing the results of the SHA3D analysis, see above.

🤝 Contributor covenant code of conduct

This project adheres to the Contributor Covenant code of conduct. By participating, you are expected to uphold this code. Please report unacceptable behavior to [e-mail].

Responsible Use: We are committed to advancing the responsible development and use of artificial intelligence. Please follow our Acceptable Use Policy when engaging with the model.

🔒 Security

If you believe you have found a security issue, please responsibly disclose by contacting us at [e-mail].