A system for performing automated high-content cell imaging, the system comprising: a stage assembly configured to receive a container having a plurality of wells containing biological cells and to automatically and selectively position each of the wells at a viewing position; a fluorophore excitation source configured to automatedly produce excitation light that is directed to the viewing position to induce fluorophore emission light from the biological cells when positioned at the viewing position; a transmission light assembly configured to automatedly produce transmission light that is directed to the viewing position to illuminate the biological cells when positioned at the viewing position; a microscope objective aligned with the viewing position to receive the induced fluorophore emission light and the transmission light that passes through the biological cells; and an imaging device configured to automatedly image and record the induced fluorophore emission light and the transmission light that passes through the biological cells, and wherein the transmission light assembly (126, 208, 250) comprises a plurality of light sources arranged about an optical axis and emitting light of different colored wavelengths, wherein the plurality of light sources comprise a plurality of light sets, each light set having a pair of light sources, the light sources (216a - 216f) are paired up in sets of two such that both light sources of a light set emit the same color or wavelength when energized, the light sources (216a - 216f) of each light set being positioned on opposite sides of the optical axis and the light sets being selectively energizable, the system further comprising a computerized device having one or more processors and memory, the computerized device being operable to perform image analysis on recorded images of the induced fluorophore emission light and the transmission light that passes through the biological cells. a stage assembly configured to receive a container having a plurality of wells containing biological cells and to automatically and selectively position each of the wells at a viewing position; a fluorophore excitation source configured to automatedly produce excitation light that is directed to the viewing position to induce fluorophore emission light from the biological cells when positioned at the viewing position; a transmission light assembly configured to automatedly produce transmission light that is directed to the viewing position to illuminate the biological cells when positioned at the viewing position; a microscope objective aligned with the viewing position to receive the induced fluorophore emission light and the transmission light that passes through the biological cells; and an imaging device configured to automatedly image and record the induced fluorophore emission light and the transmission light that passes through the biological cells, and wherein the transmission light assembly (126, 208, 250) comprises a plurality of light sources arranged about an optical axis and emitting light of different colored wavelengths, wherein the plurality of light sources comprise a plurality of light sets, each light set having a pair of light sources, the light sources (216a - 216f) are paired up in sets of two such that both light sources of a light set emit the same color or wavelength when energized, the light sources (216a - 216f) of each light set being positioned on opposite sides of the optical axis and the light sets being selectively energizable, the system further comprising a computerized device having one or more processors and memory, the computerized device being operable to perform image analysis on recorded images of the induced fluorophore emission light and the transmission light that passes through the biological cells.