John Lock

AI for Systems Microscopy

Abstract

This presentation will first introduce an exemplar Systems Microscopy (imaging-based single cell) analysis pipeline, applied to the study of cancer cells and to the understanding of links between cellular features and disease states / outcomes. Next, I will introduce a custom deep learning analysis platform based around a 2-stage variational autoencoder (developed in collaboration with Prof Erik Meijering), and describe how this tool is being extended and made ‘explainable’ by VR-based data visualisation using the novel ‘BioDive’ software developed in collaboration with Associate Professor Tomasz Bednarz, UNSW EPICentre. Finally, I will ‘zoom out’ to imagine the opportunities for a distributed yet dedicated centre of excellence for Explainable AI in Biomedical Imaging, linking UNSW researchers spanning Medicine, Engineering, CSE and beyond to enhance our shared capacity at the forefront AI applications to biomedical imaging.

Bio

Dr John Lock is Head of the Cancer Systems Microscopy lab within the School of Medical Sciences since 2018. He completed his PhD within the Institute for Molecular Bioscience at the University of Queensland, focusing on quantitative imaging of complex single cell behaviours. He began postdoctoral research at the Karolinska Institute in Stockholm with back to back fellowships from the Wenner-Gren Foundation and the Swedish Cancer Foundation, focusing on understand the links between molecular regulation, phenotype and behaviour of cancer cells. He became Assistant Professor in recognition of his role in pioneering Systems Microscopy; a pan-European effort to establish cellular imaging as a new pillar of systems biology, leading a multidisciplinary team in the application of Systems Microscopy to cancer research. Returning to Australia with a senior position in the lab of Professor Katharina Gaus at UNSW (EMBL Node for Single Molecule Science), he drove formation of a dedicated Systems Microscopy facility with funding support from the Australian Research Council and the prestigious Ramaciotti Biomedical Research Award. Forming the Cancer Systems Microscopy lab in 2018, he and his collaborators are deploying a multidisciplinary suite of tools advancing experimental automation, cellular imaging, image analysis, statistical assessment and data visualisation, to advance fundamental and clinical understanding of cancer, as well as drug discovery.