The PEET package (Particle Estimation for Electron Tomography) is a collection of Matlab programs for aligning and averaging particles in subvolumes of tomograms. It has a set of classes, written by Rick Gaudette, for accessing IMOD models and MRC image files.
The source code is located here and is open source under the GPL license, version 2. The classes are in the MatTomo directory. There is a User's Guide in the MatTomo/Docs directory as well as some documention in the individual files.