We present a new method for the non-rigid registration of serial mouse microCT images which undergo potentially large changes in the positions of the legs due to articulation. While non-rigid registration methods have been extensively used in the evaluation of individual organs, application in whole body imaging has been limited, primarily because the scale of possible displacements and deformations is large resulting in poor convergence of most methods. Our method is based on the extended demons algorithm that uses a level-set representation of the mouse skin and skeleton as an input, and composed of three steps reflecting the natural physical movements of bony structures. We applied our method to the registration of serial microCT mouse images demonstrating encouraging performances as compared to competitive techniques.