Deep learning is revolutionising pathology, offering novel opportunities in disease prognosis and personalised treatment. Historically, stain normalisation has been a crucial preprocessing step in computational pathology pipelines, and persists into the deep learning era. Yet, with the emergence of feature extractors trained using self-supervised learning (SSL) on diverse pathology datasets, we call this practice into question. In an empirical evaluation of publicly available feature extractors, we find that omitting stain normalisation and image augmentations does not compromise downstream performance, while incurring substantial savings in memory and compute. Further, we show that the top-performing feature extractors are remarkably robust to variations in stain and augmentations like rotation in their latent space. Contrary to previous patch-level benchmarking studies, our approach emphasises clinical relevance by focusing on slide-level prediction tasks in a weakly supervised setting with external validation cohorts. This work represents the most comprehensive robustness evaluation of public pathology SSL feature extractors to date, involving more than 6,000 training runs across nine tasks, five datasets, three downstream architectures, and various preprocessing setups. Our findings stand to streamline digital pathology workflows by minimising preprocessing needs and informing the selection of feature extractors.

The rapid growth of digital pathology in recent years has provided an ideal opportunity for the development of artificial intelligence-based tools to improve the accuracy and efficiency of clinical diagnoses. One of the significant roadblocks to current research is the high level of visual variability across digital pathology images, causing models to generalise poorly to unseen data. Stain normalisation aims to standardise the visual profile of digital pathology images without changing the structural content of the images. In this chapter, we explore different techniques which have been used for stain normalisation in digital pathology, with a focus on approaches which utilise generative adversarial networks (GANs). Typically, GAN-based methods outperform non-generative approaches but at the cost of much greater computational requirements. However, it is not clear which method is best for stain normalisation in general, with different GAN and non-GAN approaches outperforming each other in different scenarios and according to different performance metrics. This is an ongoing field of study as researchers aim to identify a method which efficiently and effectively normalises pathology images to make AI models more robust and generalisable.

Virtual stain transfer is a promising area of research in Computational Pathology, which has a great potential to alleviate important limitations when applying deeplearningbased solutions such as lack of annotations and sensitivity to a domain shift. However, in the literature, the majority of virtual staining approaches are trained for a specific staining or stain combination, and their extension to unseen stainings requires the acquisition of additional data and training. In this paper, we propose HistoStarGAN, a unified framework that performs stain transfer between multiple stainings, stain normalisation and stain invariant segmentation, all in one inference of the model. We demonstrate the generalisation abilities of the proposed solution to perform diverse stain transfer and accurate stain invariant segmentation over numerous unseen stainings, which is the first such demonstration in the field. Moreover, the pre-trained HistoStar-GAN model can serve as a synthetic data generator, which paves the way for the use of fully annotated synthetic image data to improve the training of deep learning-based algorithms. To illustrate the capabilities of our approach, as well as the potential risks in the microscopy domain, inspired by applications in natural images, we generated KidneyArtPathology, a fully annotated artificial image dataset for renal pathology.