TIAToolbox as an end-to-end library for advanced tissue image analytics

Background Computational pathology has seen rapid growth in recent years, driven by advanced deep-learning algorithms. Due to the sheer size and complexity of multi-gigapixel whole-slide images, to the best of our knowledge, there is no open-source software library providing a generic end-to-end API for pathology image analysis using best practices. Most researchers have designed custom pipelines from the bottom up, restricting the development of advanced algorithms to specialist users. To help overcome this bottleneck, we present TIAToolbox, a Python toolbox designed to make computational pathology accessible to computational, biomedical, and clinical researchers. Methods By creating modular and configurable components, we enable the implementation of computational pathology algorithms in a way that is easy to use, flexible and extensible. We consider common sub-tasks including reading whole slide image data, patch extraction, stain normalization and augmentation, model inference, and visualization. For each of these steps, we provide a user-friendly application programming interface for commonly used methods and models. Results We demonstrate the use of the interface to construct a full computational pathology deep-learning pipeline. We show, with the help of examples, how state-of-the-art deep-learning algorithms can be reimplemented in a streamlined manner using our library with minimal effort. Conclusions We provide a usable and adaptable library with efficient, cutting-edge, and unit-tested tools for data loading, pre-processing, model inference, post-processing, and visualization. This enables a range of users to easily build upon recent deep-learning developments in the computational pathology literature.

Johnathan Pocock, Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Srijay Deshpande, Giorgos Hadjigeorghiou, Adam Shephard, Raja Muhammad Saad Bashir, Mohsin Bilal, Wenqi Lu, David Epstein, Fayyaz Minhas, Nasir M. Rajpoot, Shan E Ahmed Raza