The goal of neuroscience is to understand how different parts of the brain are wired together and how they communicate with one another. Several recently developed techniques use a method known as autoradiography to create images of brain connectivity and function. These autoradiographic methods promise to be quantitative and comprehensive. HoweVer, the data appear as gray scale images, which presents certain data analysis problems. Through a collaborative effort between neuroscientists, engineers, and com-puter scientists, we have developed a computer-based quantitative image analysis system. We have designed an interactive menu-driven software pack-age. Our objective was to allow neuroscientists to quantitate, tabulate, and interpret the image data collected on autoradiographic files. A description of the hardware, the software package, and its application is presented.