Electron crystallography of membrane proteins records images and diffraction patterns of frozen-hydrated two-dimensional (2D) crystals. To reconstruct the high-resolution three-dimensional (3D) structure of a membrane protein, a multitude of images of 2D crystals have to be processed. Certain processing steps are thereby similar for batches of images that were recorded under similar conditions. Here we describe how the 2dx software package can be used to automate the processing of 2D crystal images, and how the 2D and 3D merging results can be used to iteratively reprocess the images. While the processing of 2D crystal images has been fully automated, the merging process is still semi-manual.