The Cube Analyzer is a group of programs designed to analyze three-dimensional tomographic data such as CT, PET and MRI scans. It is designed to work on a Unix workstation running X-windows, and was programmed in C. Cube Analyzer provides the user with an interactive system by which he can view the scans, define regions of interest (ROI), and extract data. The system can be used alone to analyze images, or combined with the elastic matching software package to analyze computer-generated ROI's.