spatialleiden 0.3.0

Implementation of multiplex Leiden for analysis of (multimodal) spatial omics data.

SpatialLeiden

SpatialLeiden is an implementation of Multiplex Leiden clustering that can be used to cluster spatially resolved omics data.

SpatialLeiden integrates with the scverse by leveraging anndata but can also be used independently.

Installation

spatialleiden is available on PyPI and bioconda.

# PyPI
pip install spatialleiden

# or conda
conda install bioconda::spatialleiden

For detailed installation instructions please refer to the documentation.

Documentation

For documentation of the package please refer to the ReadTheDocs page.

Citations

If you are using spatialleiden for your research please cite

Müller-Bötticher, N., Sahay, S., Eils, R., & Ishaque, N. (2025). SpatialLeiden: spatially aware Leiden clustering. Genome Biology, 26(1), 24. https://doi.org/10.1186/s13059-025-03489-7

@article{spatialleiden2025,
	author = {Müller-Bötticher, Niklas and Sahay, Shashwat and Eils, Roland and Ishaque, Naveed},
	title = {SpatialLeiden: spatially aware Leiden clustering},
	journal = {Genome Biology},
	year = {2025},
	month = {Feb},
	day = {07},
	volume = {26},
	number = {1},
	pages = {24},
	doi = {10.1186/s13059-025-03489-7},
	url = {https://doi.org/10.1186/s13059-025-03489-7}
}

Versioning

This project follows the SemVer guidelines for versioning.

License

This project is licensed under the MIT License - for details please refer to the LICENSE file.