Electron crystallography determines the structure of two-dimensional (2D) membrane protein crystals and other 2D crystal systems. Cryotransmission electron microscopy records high-resolution electron micrographs, which require computer processing for three-dimensional structure reconstruction. We present anew software system 2dx, which is designed as a user-friendly, platform-independent software package for electron crystallography. 2dx assists in the management of an image-processing project, guides the user through the processing of 2D crystal images, and provides transparence for processing tasks and results. Algorithims are implemented in the form of script templates reminiscent of c-shell scripts. These templates can be easily modified or replaced by the user and can also execute modular stand-alone programs from the MRC software or from other image processing software packages. 2dx is available under the GNU General Public License at 2dx.org. (c) 2006 Elsevier Inc. All rights reserved.