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InterScale

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InterScale concept

InterScale is a package for cell interaction analysis in spatial transcriptomics data. It is build on top of PyG (via geome), AnnData, scanpy squidpy and scvi-tools.

Resources

  • An installation guide, tutorials and API documentation is available in the documentation.
  • Check out our seperate reproduciblity repository to reproduce the figures for the manuscript
  • Please use issues to submit bug reports.
  • If you would like to contribute, check out the contributing guide.
  • If you find InterScale useful for your research, please consider citing the InterScale preprint.

Reference

@article{DrummerJimenez2026,
  author    = {Drummer, F. and Jimenez, S. et al.},
  title     = {InterScale reveals multi-scale cellular interaction programs in spatial transcriptomics},
  journal   = {BioArvix},
  year      = {2026},
  doi       = {10.64898/2026.05.07.723456},
  url       = {https://doi.org/10.64898/2026.05.07.723456}
}