spatialleiden 0.4.0
Implementation of multiplex Leiden for analysis of (multimodal) spatial omics data.
Requires Python: >=3.10

# SpatialLeiden

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``SpatialLeiden`` is an implementation of
[Multiplex Leiden clustering](https://leidenalg.readthedocs.io/en/stable/multiplex.html)
that can be used to cluster spatially resolved omics data.

``SpatialLeiden`` integrates with the [scverse](https://scverse.org/) by leveraging
[anndata](https://anndata.readthedocs.io/) but can also be used independently.

## Installation

`spatialleiden` is available on [PyPI](https://pypi.org/project/spatialleiden/) and
[bioconda](https://bioconda.github.io/recipes/spatialleiden/README.html).

```sh
# PyPI
pip install spatialleiden
```

```sh
# or conda
conda install bioconda::spatialleiden
```

For detailed installation instructions please refer to the
[documentation](https://spatialleiden.readthedocs.io/page/installation.html).

## Documentation

For documentation of the package please refer to the
[ReadTheDocs page](https://spatialleiden.readthedocs.io/).

## 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](https://semver.org/) 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/.