Single molecule imaging and simultaneous visualization of multi-kind molecules in cells enabled the quantification of molecular dynamics, interactions and kinetics. Immunological responses and signaling processes are visualized at the single-molecule level. Based on these three-dimensional and temporal parameters, we examine numerical modeling and computer simulations of cell functions. Using the combination of single molecule quantification and “in silico” modeling, we aim to open up new frontiers for understanding immune cells as molecular systems.