This repository is an umbrella project for computational neuroscience tools and models.
It integrates multiple approaches to studying brain networks across scales, from cross-species atlases to directed connectomes and network modeling.

All projects live under the projects/ directory. Each project includes its own README and requirements.txt.

OmniConnectModel/
├── README.md              # Top-level overview (this file)
├── LICENSE                # MIT license for the whole repository
│
└── projects/
    ├── common_cross_species_atlas/   # Common gray-matter atlas across species
    └── cross_species_connectomics/   # Directed connectomics and tracer integration

Path: projects/common_cross_species_atlas/

Contains the code and minimal data required to reproduce all quantitative analyses and figures for the Common Cross-Species Atlas.
Includes the hierarchical parcellation framework, volumetric statistics, and atlas validation metrics across mouse, marmoset, rhesus macaque, and human.

📄 Project README
📖 Citation:

A hierarchical framework for cortical and subcortical gray-matter parcellation across rodents, primates, and humans
Siva Venkadesh, Yuhe Tian, Wen-Jieh Linn, Jessica Barrios Martinez, Harrison Mansour, James Cook,
David J. Schaeffer, Diego Szczupak, Afonso C. Silva, G Allan Johnson, Fang-Cheng Yeh.
bioRxiv (2025). doi: 10.1101/2025.09.08.675002

Path: projects/cross_species_connectomics/

Framework for constructing directed connectomes by integrating mouse viral tracing with diffusion MRI across species.
Includes tractography shell scripts, connectome construction, validation, and statistical analysis code.

📄 Project README
📖 Citation:

Cross-species brain circuitry from diffusion MRI tractography and mouse viral tracing.
Siva Venkadesh, Wen-Jieh Linn, Yuhe Tian, G Allan Johnson, Fang-Cheng Yeh.
bioRxiv (2025). doi: 10.1101/2025.09.07.674762

Clone the repository:

git clone https://github.com/<your-username>/OmniConnectModel.git
cd OmniConnectModel

Install dependencies:

Each project defines its own requirements.txt for additional dependencies.

This repository is released under the MIT License.
See the LICENSE file for details.