HistoCartography: A Toolkit for Graph Analytics in Digital Pathology

Abstract

Advances in entity-graph 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 explainability. However, their analysis requires prerequisites for image-to-graph translation and knowledge of state-of-the-art 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. HistoCartography is available at https://github.com/histocartography/histocartography.