⚠️ This tool is for research purpose only!

StrokeSeg: Automated Stroke Segmentation Application

StrokeSeg is a Python application designed to automate the segmentation of stroke lesions from medical imaging data. It provides a complete workflow including preprocessing, inference using trained models, and postprocessing with visualization tools. The modular architecture allows for easy customization and extension.

Application Architecture Overview

The project is organized into several key modules, each responsible for a specific aspect of the stroke segmentation workflow:

entrypoints/: Contains the main entry points for the application, including CLI and GUI interfaces.
preprocessing/: Handles data preparation tasks such as brain extraction, resampling, and general preprocessing utilities (preprocessor.py, utils.py).
inference/: Manages the inference process, applying trained models to input data for stroke segmentation (inference.py).
postprocessing/: Includes postprocessing steps (postprocessor.py) and visualization tools (viewer.py) to refine and display segmentation results.
managers/: Provides configuration (config_manager.py) and option management (option_manager.py), as well as singleton patterns (singleton.py) for shared resources.
logger/: Implements logging functionality (logger.py) to track application events and errors.
utils/: Offers various utility functions for model management, file naming, path handling, string operations, and more.
assets/: Stores static assets such as images used in the application
logs/: Contains log files generated during application runs.

Each module is designed to be modular and maintainable, facilitating easy updates and extensions to the application's functionality.

User Guide

For detailed usage instructions, please refer to the USER_GUIDE.md file.

Setup Instructions

To set up the application, simply run the provided setup script:

./setup.sh

You do not need to manually clone the repository; the setup.sh script will handle cloning automatically. If you have already cloned the repository, make sure it is located in a parent directory named StrokeSeg.sh, and execute setup.sh from the parent of StrokeSeg.sh. The script will update the repository and install all necessary dependencies for you.