We present a new method of automatic 3D filament representation which uses stereo micrographs to reconstruct three-dimensional trajectories of filament-like objects as DNA molecules. The method deals with low contrasted and noisy images, as obtained hom cryovitrified samples by means of electron microscopy. The three-dimensional information is extracted from skeletizing simultaneously both images of a given stereo-pair, instead of processing them separately. The main advantages of the technique are reproducibility and speed, compared to the reconstruction done by manual registration, i.e., clicking on the stereo micrographs. (C) 1996 Academic Press, Inc.