Nanomaterials lacking intrinsic fluorescence are labeled with fluorophores. After adding nanoparticles to live cells or extracellular models, a confocal or epifluorescence microscope equipped with a charge-coupled device camera or photomultiplier tube is used to capture time series images at the desired temporal resolution. The movies are processed with commercial, free or custom software to generate x,y coordinate datasets to reconstruct trajectories of particles. Data are analyzed to calculate transport parameters, such as mean square displacement, diffusion coefficient and velocity.