AbstractNew simple and fast methods for 3‐D depth perception and interaction in volume visualization and quantitative analysis of dual‐fluorescence confocal microscopy images are presented. By integrating a 3‐D display and an associated 3‐D input device, a system has been developed which creates an autostereoscopic confocal microscopy workstation environment on an IBM‐compatible personal computer. The system incorporates appropriate 3‐D image processing algorithms and enables the user to interactively address subregions in the data volume to identify domains of interest for subsequent volume and distance measurements. In the analysis of chromosomes in interphase nuclei these capabilities are shown to be useful in finding distances between chromosome domains and their respect