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
scanpy and anndata
but can also be used independently.
spatialleiden is available on PyPI and
bioconda.
# PyPI
pip install spatialleiden# or conda
conda install bioconda::spatialleidenFor detailed installation instructions please refer to the documentation.
For documentation of the package please refer to the ReadTheDocs page.
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}
}
This project follows the SemVer guidelines for versioning.
This project is licensed under the MIT License - for details please refer to the LICENSE file.