A software system for interactive manipulation of three-dimensional data has been developed, based on the Open inventor tool kit. The primary use of this software system is in the segmentation of tomographic reconstructions of subcellular structures. To this end, the reconstruction is represented by volume rendering and displayed in stereo. A three-dimensional cursor with adjustable shape and size is used to define and isolate regions of interest inside the volume, based on the user's expert knowledge, Once isolated, the region of interest call be conveniently analyzed and displayed. (C) 1997 Academic Press.