Methods and systems for reconstruction of a three-dimensional representation of a moving arterial tree structure from a pair of sequences of time varying two-dimensional images thereof and for analysis of the reconstructed representation. In one aspect of the invention, a pair of time varying arteriographic image sequences are used to reconstruct a three-dimensional representation of the vascular tree structure as it moves through a cardiac cycle. The arteriographic image sequences maybe obtained from a biplane imaging system or from two sequences of images using a single plane imaging system. Another aspect of the invention then applies analysis methods and systems utilizing the three-dimensional representation to analyze various kinematic and deformation measures of the moving vascular structure. Analysis results may be presented to the user using color coded indicia to identify various kinematic and deformation measures of the vascular tree.