Please see: Zhao J, Brubaker MA, Benlekbir S, and Rubinstein JL (2015). Description and comparison of algorithms for correcting anisotropic magnification in cryo-EM images. J Struct Biol 192, 209-15 for information on how these algorithms work.
The manuscript can also be found on ArXiv: http://arxiv.org/abs/1501.05928
Note: This software is still under development. Please email John Rubinstein or subscribe to changes on this page if you want to find out about (possibly critical) updates.