We have developed a multi-mode digital imaging system (1-3) which acquires images with a 12 bit cooled CCD camera. A multiple band pass dichromatic mirror and robotically controlled excitation filter wheels provide rapid wavelength selection for epi-fluorescence with DAPI, fluorescein or GFP and X-rhodamine fluorophores while maintaining image registration on the cooled CCD detector. Shutters select illumination either by epi-fluorescence or by transmitted light for phase contrast or DIC. A robotically controlled emission filter wheel in front of the CCD camera inserts an analyzer in the light path for DIC imaging. To maximize fluorescence light intensity, the analyzer is removed and an optical flat of equivalent optical thickness is inserted for fluorescence imaging. A slider is inserted at the field diaphragm position of the fluorescence epi-illuminator to provide in-focus slit and spot targets for 360 nm photoactivation of “caged” fluorophores. The microscope system is robotically controlled and image acquisition and analysis is performed using MetaMorph™ digital imaging software.