A method of providing supercontinuum illumination in applications involving the excitation of fluorescence, comprising generating, at an optical pump laser, optical pump pulses at a pump pulse repetition rate; selectively controlling with an optical modulator the launch of pump pulses into a nonlinear optical element comprising an optical fiber at a variable, lower repetition rate to thereby selectively control the repetition rate of supercontinuum pulses generated within the optical fiber; and illuminating a sample with supercontinuum pulses to excite fluorescence. The supercontinuum pulses can be wavelength filtered such that the fluorescence is excited with wave length filtered supercontinuum pulses.