Data-driven color augmentation for H&E stained images in computational pathology

Abstract

Computational pathology targets the automatic analysis of Whole Slide Images (WSI). WSIs are high-resolution digitized histopathology images, stained with chemical reagents to highlight specific tissue structures and scanned via whole slide scanners. The application of different parameters during WSI acquisition may lead to stain color heterogeneity, especially considering samples collected from several medical centers. Dealing with stain color heterogeneity often limits the robustness of methods developed to analyze WSIs, in particular Convolutional Neural Networks (CNN), the state-of-the-art algorithm for most computational pathology tasks. Stain color heterogeneity is still an unsolved problem, although several methods have been developed to alleviate it, such as Hue-Saturation-Contrast (HSC) color augmentation and stain augmentation methods. The goal of this paper is to present Data-Driven Color Augmentation (DDCA), a method to improve the efficiency of color augmentation methods by increasing the reliability of the samples used for training computational pathology models. During CNN training, a database including over 2 million H&E color variations collected from private and public datasets is used as a reference to discard augmented data with color distributions that do not correspond to realistic data. DDCA is applied to HSC color augmentation, stain augmentation and H&E-adversarial networks in colon and prostate cancer classification tasks. DDCA is then compared with 11 state-of-the-art baseline methods to handle color heterogeneity, showing that it can substantially improve classification performance on unseen data including heterogeneous color variations.