A computer-assisted three-dimensional dynamic image analysis system (3D-DIAS) has been developed for reconstructing and motion analyzing living, crawling cells. The system simultaneously reconstructs the cell surface, the nucleus and pseudopodia, both expanding and retracting. Although this system has been developed for single cell analysis, it can be used for the dynamic reconstruction and motion analysis of cells in early embryos, the human heart and any other cell, organ or object changing shape over time. Ongoing development of a dynamic analysis system with a confocal front-end, a high speed reconstruction system, a near-real time system and a virtual reality system are described.