Single-particle tracking provides a powerful technique for measuring dynamic cellular processes on the level of individual molecules. Much recent work has been devoted to using single particle tracking to measure long-range movement of particles on the cell surface, including methods for automated localization and tracking of particles [1-3]. However, most particle tracking studies to date ignore cell surface curvature and dynamic cellular deformation, factors frequently present in physiologically relevant situations. In this report, we perform quantitative evaluation of single-particle tracking on curved and deforming cell surfaces. We also introduce a new hybrid method that uses non-rigid cellular modeling for improved computation of single-particle tracking trajectories on the surfaces of cells undergoing deformation. This method combines single-molecule and bulk fluorescence measurements in an automated manner to enable more accurate and robust characterization of dynamic cell physiology and regulation.