This invention provides a method for screening large numbers of individual cells or colonies of cells using scanning microscopy coupled with fluorescence lifetime measurement and analysis, using time-correlated single photon counting. This invention further provides an automated method for selecting cells that exhibit desired characteristics. The method uses the scanning microscope system to focus a laser beam onto a surface upon which cells are immobilized on the timescale of the procedure. The cells that are illuminated in this way are killed or their growth is inhibited. The focused laser beam is scanned across the surface and turned on and off during the scanning process such that only non-irradiated cells survive, resulting in a patterned cell growth This invention further provides a computer-controlled projection device, such as a micro-mirror array or a liquid crystal display system, which is sued to project an image onto the cells.