HistoCartography swMATH ID: 39628 Software Authors: Guillaume Jaume, Pushpak Pati, Valentin Anklin, Antonio Foncubierta, Maria Gabrani Description: HistoCartography: A Toolkit for Graph Analytics in Digital Pathology. Advances in entity-graph based analysis of histopathology images have brought in a new paradigm to describe tissue composition, and learn the tissue structure-to-function relationship. Entity-graphs offer flexible and scalable representations to characterize tissue organization, while allowing the incorporation of prior pathological knowledge to further support model interpretability and explainability. However, entity-graph analysis requires prerequisites for image-to-graph translation and knowledge of state-of-the-art machine learning algorithms applied to graph-structured data, which can potentially hinder their adoption. In this work, we aim to alleviate these issues by developing HistoCartography, a standardized python API with necessary preprocessing, machine learning and explainability tools to facilitate graph-analytics in computational pathology. Further, we have benchmarked the computational time and performance on multiple datasets across different imaging types and histopathology tasks to highlight the applicability of the API for building computational pathology workflows. Homepage: https://arxiv.org/abs/2107.10073 Source Code: https://github.com/histocartography/histocartography Dependencies: Python Keywords: Image and Video Processing; arXiv_eess.IV; Computer Vision; Pattern Recognition; arXiv_cs.CV; Graph Analytics; Digital Pathology; Graph Representation Learning; Computational Pathology; Python API Related Software: PanNuke; HoVer-Net; HACT-Net; Grad-CAM; DGL; GNNExplainer; CGC-Net; PyTorch; Torchvision; NumPy; OpenSlide; ImageNet; StainTools; HistomicsTK; QuPath; histolab; Python Cited in: 0 Publications Standard Articles 1 Publication describing the Software Year HistoCartography: A Toolkit for Graph Analytics in Digital Pathology Guillaume Jaume, Pushpak Pati, Valentin Anklin, Antonio Foncubierta, Maria Gabrani 2021