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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