An automated image acquisition and analysis system has been developed that rapidly determines regional blood flow by using the locations of fluorescent microspheres deposited in tissue. A motor-driven microtome removes sections of frozen tissues in steps variable between 10 and 100 mu m. Filtered light excites microsphere fluorescence from the exposed surface of the remaining tissue block. A charge coupled device camera records fluorescence images from the tissue block surface after removal of each slice. Approximately 450 images are analyzed from perfused rat hearts providing precise x, y, and z locations of about 10 000 microspheres. Image analysis of fluorescent microspheres is much faster and less labor intensive than traditional indirect microsphere-based flow measurements while providing higher quality data.