scGPT-spatial: Continual Pretraining of Single-Cell Foundation Model for Spatial Transcriptomics

 

🟩 TL,DR Highlights 🟩

✨ Spatial-omic foundation model ✨ ✨ Continual pretraining of scGPT on 30 million cells/spots ✨

✨ Novel MoE (Mixture of Experts) decoders ✨ ✨ Spatially-aware sampling ✨ ✨ Neighborhood-based reconstruction objective ✨

✨ Curation of SpatialHuman30M corpus ✨ ✨ Visium, Visium HD, Xenium, MERFISH ✨

✨ Multi-modal and multi-slide integration ✨ ✨ Cell-type deconvolution ✨ ✨ Missing gene imputation ✨

🟫 Model Weights 🟫

scGPT-spatial V1 weights on figshare.

🟦 Setup and Tutorials 🟦

To start, clone the current repo:

git clone https://github.com/bowang-lab/scGPT-spatial

Special acknowledgement to the scGPT codebase - for environment setup please follow instructions there.

Check out our zero-shot inference tutorial on github! More code coming soon.

🟪 Preprint and Citation 🟪

Check out our preprint! https://www.biorxiv.org/content/10.1101/2025.02.05.636714v1