The Semper system was developed 20 years ago to address problems of 2-D image averaging and transfer function correction. User extendibility was an important design requirement, and a very considerable body of extensions have been written in the interim; this paper reviews those most relevant to macromolecular structure determination by 2-D and 3-D electron microscopy. The techniques best provided for are distortion-compensated averaging (correlation averaging and local unbending), selective averaging (of several kinds), 3-D reconstruction of 2-D crystals, and transfer function estimation and correction. The (normally interactive) control language is flexible enough to be a frequently preferred alternative to programming at any lower level. (C) 1996 Academic Press, Inc.