A method for correcting distortion in a coherent electron diffraction imaging (CEDI) image induced by a projection lens makes use of a known secondary material that is imaged together with a sample of interest. Reflections generated from the secondary material are located in the image, and these observed reflections are used to approximate a beam center location. Using a known lattice structure of the secondary material, Friedel pairs are located in the image and unit cell vectors are identified. Predicted positions for each of the secondary material reflections are then determined, and the position differences between the observed reflections and the predicted reflections are used to construct a relocation function applicable to the overall image. The relocation function is then used to adjust the position of image components so as to correct for the distortion.