The ability to visualize protein dynamics and biological processes by in vivo microscopy is revolutionizing many areas of biology. These methods generate large, kinetically complex data sets, which often cannot be intuitively interpreted. The combination of dynamic imaging and computational modelling is emerging as a powerful tool for the quantitation of biophysical properties of molecules and processes. The new discipline of computational cell biology will be essential in uncovering the pathways, mechanisms and controls of biological processes and systems as they occur in vivo.