Systems and methods for delineating anatomical boundaries from two- and three-dimensional image data are described. A template shape is used to examine new image element (e.g. pixel and/or voxel) locations and determine boundary intersection based on characteristics determined from the plurality of image elements contained within this template. The result is a polyline/surface delineation of the desired anatomy, which can be used for morphometric/shape analysis, patient specific output, and knowledge-based queries.