BrainParcellation

This is a comprehensive codebase designed for generating whole-brain fine-grain sub-parcellation based on dendritic microenvironments. This repository is maintained mainly by Yufeng Liu (yufeng_liu@seu.edu.cn) and Sujun Zhao from SEU-ALLEN, with the help from Zuo-Han Zhao, and Zhixi Yun.

The package was released along with our paper, which is currently archived on biorxiv (https://www.biorxiv.org/content/10.1101/2024.09.22.614330v1) and is in review. For more details, please refer to the paper.

Getting Started

Prerequisites

• Python. The project is developed under Python 3.10 and should be compatible with Python versions 3.6 and above.
• Common python packages for data processing and visualization, including NumPy, SciPy, scikit-learn, scikit-image, pandas, seaborn, matplotlib, etc.
• pylib. pylib is a customized library developed by Yufeng Liu and Zuo-Han Zhao for neuronal file parsing, image processing, morphology analysis, anatomical processing, and other specialized utilities for neuron informatics. You can download it from GitHub (git@github.com:SEU-ALLEN-codebase/pylib.git) and add the directory to your $PYTHONPATH.
• Other dependencies are listed in requirements.txt

Installation

Clone the repository and install the necessary dependencies:

git clone https://github.com/SEU-ALLEN-codebase/BrainParcellation.git
cd BrainParcellation
pip install -r requirements.txt

Structure of the project

The structure of the outermost levels of the source code and examples is as follows:

BrainParcellation/
│
├── common_lib/              # Common tools and variables
│   └── configs.py                 
├── evaluation/              # Evaluation of the reconstructions
├── microenviron/            # The core utilities, including microenvironment construction and sub-parcellation.
├── reconstruction/          # Source codes and examples for neuron reconstruction.
├── coplanarity/             # Coplanarity of local branches. [Deprecated]
├── requirements.txt         # List of dependencies
├── README.md                # Project overview and instructions
├── LICENSE                  # License information
└── .gitignore               # Git ignore file

For detailed information on each section, please refer to the README.md file located within that section.

Usage

This repository contains an analytical framework with various tools. You can simply navigate to the specific script and run it according to the instructions provided in the corresponding README file.

License

This project is licensed under the MIT License. See the LICENSE file for more details.

Acknowledgments

Special thanks to all contributors and the SEU-ALLEN team for their support in developing this project.