NicheCompass (Niche Identification based on Cellular grapH Embeddings of COMmunication Programs Aligned across Spatial Samples) is a package for end-to-end analysis of spatial multi-omics data, including spatial atlas building, niche identification & characterization, cell-cell communication inference and spatial reference mapping. It is built on top of PyG and AnnData.

Resources

• An installation guide, tutorials and API documentation is available in the documentation.
• Please use issues to submit bug reports.
• If you would like to contribute, check out the contributing guide.
• If you find NicheCompass useful for your research, please consider citing the NicheCompass manuscript.

Reference

@article{Birk2025,
  author    = {Birk, S. and Bonafonte-Pard{\`a}s, I. and Feriz, A. M. and et al.},
  title     = {Quantitative characterization of cell niches in spatially resolved omics data},
  journal   = {Nature Genetics},
  year      = {2025},
  doi       = {10.1038/s41588-025-02120-6},
  url       = {https://doi.org/10.1038/s41588-025-02120-6}
}