cryoCOFI

Overview

cryoCOFI (CarbOn FIlm detector for cryo-EM images) is a script designed for cryo-EM images & cryo-ET tomograms to detect carbon films and get rid of particles inside them.

Features

• Carbon film detection and particle screening in cryo-EM images
• Improved algorithm for edge detection (Bilateral filter + Canny detector, aka Bicanny)
• Integration with Dynamo (.doc and .tbl files) & cryoSPARC
• GPU-accelerated image processing using CuPy and CUDA

Requirements

• Python 3.9+
• CUDA-compatible GPU
  • CUDA Toolkit 11.1 or later
  • NVIDIA GPU Driver supporting CUDA 12.2 or later
• CuPy, >=13.3.0
• NumPy, >=2.0.2
• pandas, >=2.2.3

Installation

Via git clone

1. Clone the repository:

   git clone https://github.com/ZhenHuangLab/cryoCOFI.git
   

2. Navigate to the project directory:

   cd cryoCOFI
   

3. Install the package:

   pip install .
   

Via pip

pip install cryoCOFI

Usage

cryoCOFI can be used as a command-line tool:

cryoCOFI [command] [options]

Available commands:

• readmrc: Process a single MRC file
• readdynamo: Process Dynamo .doc and .tbl files
• readcs: Process cryoSPARC .cs files

For detailed usage instructions, run:

cryoCOFI [command] --help

License

This script is licensed under GPLv3.

Contributing

Contributions to cryoCOFI are welcome! Please feel free to submit a Pull Request.

Contact

For questions or support, please contact: zhen.victor.huang@gmail.com

For more information, visit: https://github.com/ZhenHuangLab/cryoCOFI