Welcome to the histocartography repository! 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.
If you encounter any issue or have questions regarding the library, feel free to open a GitHub issue. We'll do our best to address it.
Installation
PyPI installer (recommended)
pip install histocartography
Development setup
- Clone the repo:
git clone https://github.com/histocartography/histocartography.git && cd histocartography
- Create a conda environment:
conda env create -f environment.yml
- Activate it:
conda activate histocartography
- Add
histocartographyto your python path:
export PYTHONPATH="<PATH>/histocartography:$PYTHONPATH"
Tests
To ensure proper installation, run unit tests as:
python -m unittest discover -s test -p "test_*" -v
Running tests on cpu can take up to 20mn.
Using histocartography
The histocartography library provides a set of helpers grouped in different modules, namely preprocessing, ml, visualization and interpretability.
For instance, in histocartography.preprocessing, building a cell-graph from an H&E image is as simple as:
>> from histocartography.preprocessing import NucleiExtractor, DeepFeatureExtractor, KNNGraphBuilder
>>
>> nuclei_detector = NucleiExtractor()
>> feature_extractor = DeepFeatureExtractor(architecture='resnet34', patch_size=72)
>> knn_graph_builder = KNNGraphBuilder(k=5, thresh=50, add_loc_feats=True)
>>
>> image = np.array(Image.open('docs/_static/283_dcis_4.png'))
>> nuclei_map, _ = nuclei_detector.process(image)
>> features = feature_extractor.process(image, nuclei_map)
>> cell_graph = knn_graph_builder.process(nuclei_map, features)
The output can be then visualized with:
>> from histocartography.visualization import OverlayGraphVisualization, InstanceImageVisualization
>> visualizer = OverlayGraphVisualization(
... instance_visualizer=InstanceImageVisualization(
... instance_style="filled+outline"
... )
... )
>> viz_cg = visualizer.process(
... canvas=image,
... graph=cell_graph,
... instance_map=nuclei_map
... )
>> viz_cg.show()
A list of examples to discover the capabilities of the histocartography library is provided in examples. The examples will show you how to perform:
- stain normalization with Vahadane or Macenko algorithm
- cell graph generation to transform an H&E image into a graph-based representation where nodes encode nuclei and edges nuclei-nuclei interactions. It includes: nuclei detection based on HoverNet pretrained on PanNuke dataset, deep feature extraction and kNN graph building.
- tissue graph generation to transform an H&E image into a graph-based representation where nodes encode tissue regions and edges tissue-to-tissue interactions. It includes: tissue detection based on superpixels, deep feature extraction and RAG graph building.
- feature cube extraction to extract deep representations of individual patches depicting the image
- cell graph explainer to generate an explanation to highlight salient nodes. It includes inference on a pretrained CG-GNN model followed by GraphGradCAM explainer.
A tutorial with detailed descriptions and visualizations of some of the main functionalities is provided here as a notebook.
External Ressources
Learn more about GNNs
- We have prepared a gentle introduction to Graph Neural Networks. In this tutorial, you can find slides, notebooks and a set of reference papers.
- For those of you interested in exploring Graph Neural Networks in depth, please refer to this content or this one.
Papers already using this library
- Hierarchical Graph Representations for Digital Pathology, Pati et al., preprint, 2021. [pdf] [code]
- Quantifying Explainers of Graph Neural Networks in Computational Pathology, Jaume et al., CVPR, 2021. [pdf] [code]
- Learning Whole-Slide Segmentation from Inexact and Incomplete Labels using Tissue Graphs, Anklin et al., preprint, 2021. [pdf] [code]
If you use this library, please consider citing:
@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}
}
116 Dec 14, 2022
6 Dec 25, 2022
135 Dec 28, 2022
2.6k Dec 31, 2022
2.1k Dec 27, 2022
17 Nov 10, 2022
5 Jul 08, 2022
164 Dec 30, 2022
93 Dec 08, 2022
348 Dec 22, 2022
8 Dec 30, 2022
10 Oct 10, 2022
284 Dec 21, 2022
722 Dec 28, 2022
140 Dec 15, 2022
36 Dec 12, 2022
260 Dec 28, 2022
61 Dec 28, 2022
1 Jan 31, 2022
42 Sep 26, 2022