This book provides a comprehensive introduction to the range of quantitative imaging methods used in the clinic and lab to help guide outcomes and understand the impact of key biological mechanisms. It develops for the reader the methodologies, algorithmic and mathematical frameworks, and workflows used in the analysis of cell and tissue images. Case studies are incorporated throughout to show how the methods are applied in real situations to define phenotypes and associate them with specific outcomes. The chapters cover four major areas: image-based cytometry, tissue architecture, cellular dynamics, and the molecular context.