3-D Reconstruction of Macroscopic Optical Brain Slice Images

We present a method for reconstruction of macroscopic optical images of post-mortem brain slices to form a 3-D volume. This forms a key part of a series of procedures to allow post mortem findings to be accurately registered with MR images, and more generally provides a method for 3-D mapping of the distribution of pathological changes throughout the brain. In this preliminary work, four brains from a study of Creutzfeldt-Jakob disease were examined. After brain fixation, the pathologist cut coronal slices several mm thick through the brain. The anterior and posterior faces of each slice were photographed. We show that the 2-D co-registration of each such pair of images was most effectively obtained if the slice was placed in a jig before photographing. Fiducials on the jig were detected automatically and point-based rigid registration computed. For co-registration between slices, i.e., across a single cut, an intensity-based method for 2-D non-rigid registration is used which provided satisfactory results. By propagating the 2-D registrations through the volume and using the known slice thickness, the 3-D volume was reconstructed.