The CytoClone system applies phase contrast and fluorescence imaging technology to the isolation and analysis of pure cell clones. Generating high resolution cell imagery in real time, it allows users to select target cells using morphologic or structural criteria, rather than with simple fluorescence intensity values alone. Target cells may be defined and identified, for example, by the location of key cellular proteins on or within the cell, or by their association with other proteins of interest. Since each cell is imaged directly on the CytoClone during a selection run, its single cell status may be verified quickly and unequivocally.