# 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](https://www.gnu.org/licenses/gpl-3.0.en.html).
## 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
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