FuseMap

Integrate spatial transcriptomics with universal gene, cell, and tissue embeddings.

Current manuscript: An agentic AI spatial molecular foundation model of the brain. See release notes for the distinction between the manuscript workflows and the current software, including anchor alignment and Agent v2.

Manuscript code and data

Reproducibity

For manuscript analysis code, see paper_code. The current manuscript describes a frozen code and analysis archive at Zenodo. Use that archive and its run configurations for paper reproduction.

Exploratory analysis

We provide an interactive online database of the molCCF.

System Requirements

Hardware requirements

FuseMap package requires a standard computer with optional GPU to support the in-memory operations.

Software requirements

OS Requirements

This package is supported for Linux. The package has been tested on the following system:

• Linux: Ubuntu 20.04

Python Dependencies

FuseMap mainly depends on the Python scientific stack.

dgl
numpy
scipy
scikit-learn
pandas
pytorch
scanpy
seaborn

Installation and Tutorial

Use Python 3.9–3.11 (3.10 recommended). Install this checkout with:

python -m pip install .

For notebook dependencies, use python -m pip install ".[tutorials]". The PyPI package is installed with python -m pip install fusemap; see the release notes for this checkout's version.

import fusemap
fusemap.integrate("./data", "./output")

The classic Agent uses python -m pip install ".[agent]" from this repository. Agent v2 uses a separate environment and a registered scientific kernel; follow the Agent setup instructions.

• Read the FuseMap tutorial here.
• FuseMap-Agent set up tutorial here.

Citation

The current manuscript is titled An agentic AI spatial molecular foundation model of the brain. The earlier public preprint can be cited as:

Yichun He, Hao Sheng, Hailing Shi, Wendy Xueyi Wang, Zefang Tang, Jia Liu, Xiao Wang. Towards a universal spatial molecular atlas of the mouse brain. Preprint at bioRxiv https://www.biorxiv.org/content/10.1101/2024.05.27.594872v1 (2024).