This paper presents a software framework for the registration and visualization of layered image sets. To demonstrate the utility of these tools, we apply them to the St. Chad Gospels manuscript, relying on images of each page of the document as it appeared over time. An automated pipeline is used to perform non-rigid registration on each series of images. To visualize the differences between copies of the same page, a registered image viewer is constructed that enables direct comparisons of registered images. The registration pipeline and viewer for the resulting aligned images are generalized for use with other data sets.