Application, Optimisation and Evaluation of Deep Learning for Biomedical Imaging

Abstract: Microscopy imaging is a powerful technique when studying biology at a cellular and sub-cellular level. When combined with digital image analysis it creates an invaluable tool for investigating complex biological processes and phenomena. However, imaging at the cell and sub-cellular level tends to generate large amounts of data which can be difficult to analyse, navigate and store. Despite these difficulties, large data volumes mean more information content which is beneficial for computational methods like machine learning, especially deep learning. The union of microscopy imaging and deep learning thus provides numerous opportunities for advancing our scientific understanding and uncovering interesting and useful biological insights.The work in this thesis explores various means for optimising information extraction from microscopy data utilising image analysis with deep learning. The focus is on three different imaging modalities: bright-field; fluorescence; and transmission electron microscopy. Within these modalities different learning-based image analysis and processing techniques are explored, ranging from image classification and detection to image restoration and translation. The main contributions are: (i) a computational method for diagnosing oral and cervical cancer based on smear samples and bright-field microscopy; (ii) a hierarchical analysis of whole-slide tissue images from fluorescence microscopy and introducing a confidence based measure for pixel classifications; (iii) an image restoration model for motion-degraded images from transmission electron microscopy with an evaluation of model overfitting on underlying textures; and (iv) an image-to-image translation (virtual staining) of cell images from bright-field to fluorescence microscopy, optimised for biological feature relevance. A common theme underlying all the investigations in this thesis is that the evaluation of the methods used is in relation to the biological question at hand.