Shape and function are intricately related in biology. We present three biological case studies where the goal is to quantify shape change in order to analyze how shape informs function. The biologists have specific questions they are interested in answering, and have domain knowledge that should be incorporated into the the shape correspondence algorithm. We show how we incorporate these constraints into the shape matching algorithms in order to provide our collaborators with biologically-meaningful shape correspondences. Case study 1: Using strain to track ferret brain development. Case study 2: Using geodesic distances and an approximate medial axis to track an in-vivo beating chicken hearts at an early stage of development (peristaltic motion). Case study 3: Shape space based on natural neighbor coordinates for bat pinnae and noseleaves.