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.

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Oral squamous cell carcinoma (OSCC) is amongst the most common cancers, with more than 377,000 new cases worldwide each year. OSCC prognosis remains poor, related to cancer presentation at a late stage, indicating the need for early detection to improve patient prognosis. OSCC is often preceded by a premalignant state known as oral epithelial dysplasia (OED), which is diagnosed and graded using subjective histological criteria leading to variability and prognostic unreliability. In this work, we propose a deep learning approach for the development of prognostic models for malignant transformation and their association with clinical outcomes in histology whole slide images (WSIs) of OED tissue sections. We train a weakly supervised method on OED cases (n = 137) with malignant transformation (n = 50) and mean malignant transformation time of 6.51 years ( ± 5.35 SD). Stratified five-fold cross-validation achieved an average area under the receiver-operator characteristic curve (AUROC) of 0.78 for predicting malignant transformation in OED. Hotspot analysis revealed various features of nuclei in the epithelium and peri-epithelial tissue to be significant prognostic factors for malignant transformation, including the count of peri-epithelial lymphocytes (PELs) (p < 0.05), epithelial layer nuclei count (NC) (p < 0.05), and basal layer NC (p < 0.05). Progression-free survival (PFS) using the epithelial layer NC (p < 0.05, C-index = 0.73), basal layer NC (p < 0.05, C-index = 0.70), and PELs count (p < 0.05, C-index = 0.73) all showed association of these features with a high risk of malignant transformation in our univariate analysis. Our work shows the application of deep learning for the prognostication and prediction of PFS of OED for the first time and offers potential to aid patient management. Further evaluation and testing on multi-centre data is required for validation and translation to clinical practice.

The detection of mitotic figures from different scanners/sites remains an important topic of research, owing to its potential in assisting clinicians with tumour grading. The MItosis DOmain Generalization (MIDOG) 2022 challenge aims to test the robustness of detection models on unseen data from multiple scanners and tissue types for this task. We present a short summary of the approach employed by the TIA Centre team to address this challenge. Our approach is based on a hybrid detection model, where mitotic candidates are segmented, before being refined by a deep learning classifier. Cross-validation on the training images achieved the F1-score of 0.816 and 0.784 on the preliminary test set, demonstrating the generalizability of our model to unseen data from new scanners.

Computational Pathology (CPath) has seen rapid growth in recent years, driven by advanced deep learning (DL) algorithms. These algorithms typically share the same sequence of steps. However, due to the sheer size and complexity of handling large multi-gigapixel whole-slide images, there is no open-source software library that provides a generic end-to-end API for pathology image analysis using best practices for CPath. Most researchers have designed custom pipelines from the bottom-up, restricting the development of advanced CPath algorithms to specialist users. To help overcome this bottleneck, we present TIAToolbox, a Python toolbox designed to make CPath more accessible to new and advanced CPath scientists and pathologists alike. 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 all kinds of users to easily build upon recent DL developments in the CPath literature. TIAToolbox provides a user-friendly modular API to enable seamless integration of advanced DL algorithms. We show with the help of examples how state-of-the-art DL algorithms can be streamlined using TIAToolbox.