cryoblob 2025.5.26

Particle Picking of Cryo-EM Datasets

cryoblob

cryoblob is a JAX-based, JIT-compiled, scalable package for detection of amorphous blobs in low SNR cryo-EM images.

Features

• JAX-powered: Leverages JAX for high-performance computing with automatic differentiation
• GPU acceleration: Can utilize both CPUs and GPUs for processing
• Adaptive filtering: Includes adaptive Wiener filtering and thresholding
• Blob detection: Advanced blob detection using Laplacian of Gaussian (LoG) methods
• Batch processing: Memory-optimized batch processing for large datasets
• Validation: Comprehensive parameter validation using Pydantic models

Installation

pip install cryoblob

Quick Start

import cryoblob as cb

# Load an MRC file
mrc_image = cb.load_mrc("your_file.mrc")

# Process a folder of images
results = cb.folder_blobs("path/to/folder/")

# Plot results
cb.plot_mrc(mrc_image)

Package Structure

The cryoblob package is organized into the following modules:

• adapt: Adaptive image processing with gradient descent optimization
• blobs: Core blob detection algorithms and preprocessing
• files: File I/O operations and batch processing
• image: Basic image processing functions (filtering, resizing, etc.)
• plots: Visualization functions for MRC images and results
• types: Type definitions and PyTree structures
• valid: Parameter validation using Pydantic models

Package Organization

• The codes are located in /src/cryoblob/
• The notebooks are located in /tutorials/

Documentation

For detailed API documentation and tutorials, visit: https://cryoblob.readthedocs.io

License

This project is licensed under the MIT License - see the LICENSE file for details.

Authors

• Debangshu Mukherjee ([e-mail])
• Alexis N. Williams ([e-mail])