toolscverse ecosystemJune 11, 2026
Novae
Novae is a graph-based foundation model for spatial transcriptomics data, published in Nature Methods (2025) and integrated into the scverse ecosystem. It is a self-supervised graph attention network enabling zero-shot or fine-tuned spatial domain identification, native batch-effect correction across technologies, and spatially variable gene and pathway analysis. Trained on ~30 million cells across 18 tissues from Xenium, MERSCOPE, and CosMX platforms.
Novae
Graph-based foundation model for spatial transcriptomics, published in Nature Methods (2025).
- Self-supervised graph attention network architecture
- Zero-shot spatial domain identification — no external clustering needed
- Cross-technology batch-effect correction (Xenium, MERSCOPE, CosMX)
- Spatially variable gene and pathway analysis
- Trained on ~30M cells across 18 tissue types
- Part of the scverse ecosystem; installable via
pip install novae