Welcome to histocartography’s documentation!

histocartography is a python-based library designed to facilitate the development of graph-based computational pathology pipelines. The library includes plug-and-play modules to perform:

  • standard histology image pre-processing (e.g., stain normalization, nuclei detection, tissue detection)

  • entity-graph representation building (e.g. cell graph, tissue graph, hierarchical graph)

  • modeling Graph Neural Networks (e.g. GIN, PNA)

  • feature attribution based graph interpretability techniques (e.g. GraphGradCAM, GraphGradCAM++, GNNExplainer)

  • visualization tools

All the functionalities are grouped under a user-friendly API.

Contents:

Indices and tables

Reference

If you use histocartography in your projects, please cite the following:

@inproceedings{pati2021,
    title = {Hierarchical Graph Representations for Digital Pathology},
    author = {Pushpak Pati, Guillaume Jaume, Antonio Foncubierta, Florinda Feroce, Anna Maria Anniciello, Giosuè Scognamiglio, Nadia Brancati, Maryse Fiche, Estelle Dubruc, Daniel Riccio, Maurizio Di Bonito, Giuseppe De Pietro, Gerardo Botti, Jean-Philippe Thiran, Maria Frucci, Orcun Goksel, Maria Gabrani},
    booktitle = {https://arxiv.org/pdf/2102.11057},
    year = {2021}
}