3: Data Alignment

Two dimensional digital images of the stained sections were brought roughly into register with their corresponding blockface images using automated software tools produced at LONI. The preregistration program (register2D) produced an initialization file for Automated Image Registration 4.0, which completed registration using a four-parameter linear transformation. Once the registered images were reconstructed into a three-dimensional volume, the resulting volume was brought into register with an inherently three-dimensional uMRI in a defined and common coordinate system. All image processing was done on a 32-processor Onyx 200 supercomputer (SGI).