We develop and use automated super-resolution fluorescence imaging techniques combined with live cell imaging and single molecule tracking. Our experiments reveal the biophysical principles underlying the dynamic organization of cellular organelles and protein assemblies. We achieve this by collecting large datasets containing super-resolved images of thousands of single organelles or assemblies, to capture their diverse behaviors, as well as to identify emergent patterns. A major focus is the dynamics and organization of mitochondria, and how their division is patterned and their fates determined.