A software package is presented that was primarily developed for electron tomography in biological research. It comprises routines for preprocessing micrographs, CTF-correction of images of untilted and tilted specimens, alignment of tilt series, 3D reconstruction, spatial averaging of paracrystalline specimens, alignment of single particles or components of larger macromolecular assemblies, correlation averaging, multivariate statistical analysis, classification, and volume reassembly, in which molecular components in raw tomograms are replaced by averaged versions with higher signal-to-noise ratio. The emphasis for image analysis is placed on the processing of large sets of individual molecular Volumes. The design philosophy of the software is both simplicity and interoperability, i.e. to write standalone programs for simple tasks that are combined through shell scripting to provide more complex functionality, and to communicate with other software via common image formats. This paper gives an overview of the current state of the progams and some applications to cryo-electron tomography. (c) 2006 Elsevier Inc. All rights reserved.