This repository is the official implementation for the paper: SpatialAgent: An autonomous AI agent for spatial biology. Contact wang.hanchen@gene.com or hanchenw@stanford.edu if you have any questions.
We present SpatialAgent, an autonomous AI agent dedicated for spatial-biology. SpatialAgent integrates large language models with dynamic tool execution and adaptive reasoning. SpatialAgent spans the entire research schema, from experimental design to multimodal data analysis and hypothesis generation.
@article {spatialagent,
author = {Hanchen Wang and Yichun He and Coelho Paula and Matthew Bucci and other},
title = {SpatialAgent: An autonomous AI agent for spatial biology},
doi = {10.1101/2025.04.01.646459},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2025/04/01/2024.04.01.646459}
journal = {bioRxiv},
year = {2025},
}under construction
SpatialAgent_dev/
├── data/ # Data
├── src/
│ ├── baseline/ # Baseline methods
│ ├── evaluation/ # Evaluation kit
│ ├── interface/ # Graphical user inteface
│ ├── script/ # Scripts to run representative tasks
│ ├── spatialagent/
│ │ ├── agents/ # Agents
│ │ ├── plans/ # Plan templates
│ │ ├── tools/ # Tools
│ │ ├── init.py # Reorganized to final working version
│ │ ├── config.py # Configurations
│ │ └── logger.py # Logger
│ └── main.py
│
├── .gitignore # Git ignore
├── README.md # Readme
├── chatui.sh # Chat mode launch script
├── consoleui.sh # Console mode launch script
├── env.yml # Environment dependencies
├── setup.sh # All u need for setup
├── watcher.py # Watcher to automatically reload while running GUI
└── teaser.png