NicheCompass
Graph deep learning model that learns cell embeddings from communication programs to identify niches across spatial samples.
| Category | Spatial omics |
|---|---|
| GitHub | Lotfollahi-lab/nichecompass |
| First public | 2022-07-15 (source) |
| Paper | https://doi.org/10.1038/s41588-025-02120-6 · Nature Genetics (2025) |
| License | BSD-3-Clause |
| Pricing | Open source |
| Tags | #deep-learning#graph-neural-networks#spatial-omics |
| Last checked | 2026-10-16 |
Specs
| Platforms supported | Xenium, MERFISH, Slide-seq, Visium, spatial ATAC |
|---|---|
| Resolution | Single-cell / spot |
| Tasks | Niche identification, cell-cell communication, reference mapping |
| GitHub stars | 131 |
| Interface | — |
Specs come from each project's README, paper or official page · NicheCompass README · NicheCompass paper. “—” means we couldn't verify it.
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