Traditional methods to analyze image data from PET, CT and MRI have proven only partially successful. Our goals are to reformulate, extend or develop new techniques, which are mathematically and statistically well founded, that can be easily and clearly applied by a researcher or clinician to analyze these data. A review of the data-processing path from image acquisition to final analysis has been completed, resulting in the identification of a number of important areas which are currently under investigation: (1) correction of image distortion, (2) problems with traditional region of interest (ROI) analysis, (3) superposition of functional and structural images, and (4) operator supported and fully automated data extraction from images.