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:

• histocartography package
  • histocartography.pipeline module
    • Summary
    • Reference
  • histocartography.interpretability package
    • histocartography.interpretability.base_explainer module
    • histocartography.interpretability.grad_cam module
    • histocartography.interpretability.graph_pruning_explainer module
    • histocartography.interpretability.lrp_gnn_explainer module
    • Summary
    • Reference
  • histocartography.metrics package
    • histocartography.metrics.metrics module
    • Summary
    • Reference
  • histocartography.ml package
    • histocartography.ml.layers package
    • histocartography.ml.models package
    • Summary
    • Reference
  • histocartography.preprocessing package
    • histocartography.preprocessing.assignment_matrix module
    • histocartography.preprocessing.feature_extraction module
    • histocartography.preprocessing.graph_builders module
    • histocartography.preprocessing.io module
    • histocartography.preprocessing.nuclei_concept_extraction module
    • histocartography.preprocessing.nuclei_extraction module
    • histocartography.preprocessing.stain_normalizers module
    • histocartography.preprocessing.stats module
    • histocartography.preprocessing.superpixel module
    • histocartography.preprocessing.tissue_mask module
    • histocartography.preprocessing.utils module
    • Summary
    • Reference
  • histocartography.utils package
    • histocartography.utils.draw_utils module
    • histocartography.utils.graph module
    • histocartography.utils.image module
    • histocartography.utils.io module
    • histocartography.utils.torch module
    • Summary
    • Reference
  • histocartography.visualization package
    • histocartography.visualization.visualization module
    • Summary
    • Reference
  • Summary
  • Reference

Indices and tables

• Index

• Module Index

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}
}