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

Copyright (C) 2025 N. Müller-Bötticher, S. Sahay, N. Ishaque, R. Eils, HiDiHlabs

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.