An accurate, computationally efficient, and fully automated algorithm for the alignment of two-dimensional (2-D) serially acquired sections forming a three-dimensional (3-D) volume is presented. The approach relies on the optimization of a global energy function, based on the object shape, measuring the similarity between a slice and its neighborhood in the 3-D volume. Slice similarity is computed using the distance transform measure in both directions. No particular direction is privileged in the method avoiding global offsets, biases in the estimation and error propagation. The method was evaluated on real images [medical, biological, and other computerized tomography (CT) scanned 3-D data] and the experimental results demonstrated its accuracy as reconstuction errors are less than one degree in rotation and less than one pixel in translation.