A method for three-dimensional reconstruction of a branched object from a rotational sequence of images of the branched object includes segmenting the branched object from each image of the sequence, extracting centerlines of the branched object, performing symbolic reconstruction via a stereo correspondence matching between the centerlines from different views of the sequence of images using a graph cut-based optimization, and creating a three-dimensional tomographic reconstruction of the branched object compensated for motion of the branched object between the images of the sequence.