phonchi / Cryo-forum

A Framework for Orientation Recovery with Uncertainty Measurement in Cryo-EM Image Analysis

Cryo-forum

A Framework for Orientation Recovery with Uncertainty Measurement in Cryo-EM Image Analysis

Cryo-forum is a framework designed to facilitate experimentation with various strategies for orientation recovery in cryo-electron microscopy (cryo-EM).

Manuscript

• Cryo-forum: A Framework for Orientation Recovery with Uncertainty Measurement in Cryo-EM Image Analysis
  • Author: Szu-Chi Chung
  • Read the Manuscript

How to Use the Library

Installation

Prerequisite: If you do not have the Anaconda Python distribution, install it here.

Create a Conda Environment for Cryo-forum:

• More information on managing conda environments can be found here.

conda create --name cryoforum python=3.10
conda activate cryoforum

Install Dependencies:

pip install mrcfile wandb ipyvolume seaborn tensorflow_probability==0.20.0 tensorflow==2.12 tensorflow-graphics tensorflow_similarity scikit-image ipython_genutils notebook quaternion

Setup

Clone the Repository and Change Directory:

git clone https://github.com/phonchi/Cryo-forum.git
cd Cryo-forum

Tutorials and Guides

• Explore the Example Notebook for detailed documentation and analysis on both synthetic and real datasets.

Data and Pretrained Model

• Access the pretrained model and data at Pretrained Model and Data respectively.

License

Cryo-forum is released as open source software under the GNU General Public License, Version 3.

Credits

• This code base builds upon the work developed by Jelena Banjac and the code available at Bingham Rotation Learning Repository.
• The visualization code for the Bingham distribution is adapted from this source.