CarbOn FIlm detector for cryo-EM images
Project description
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 data formats (.doc and .tbl files)
- GPU-accelerated image processing using CuPy and CUDA
Requirements
- Python 3.9+
- CUDA-compatible GPU, >=12.2
- CuPy, >=13.3.0
- NumPy, >=2.0.2
- pandas, >=2.2.3
Installation
Via git clone
-
Clone the repository:
git clone https://github.com/ZhenHuangLab/cryoCOFI.git
-
Navigate to the project directory:
cd cryoCOFI
-
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 filereaddynamo
: Process Dynamo .doc and .tbl files
For detailed usage instructions, run:
cryoCOFI [command] --help
License
[Insert your chosen license here]
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
Project details
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