1. An imaging system configured to generate images of a reaction within a microchannel of a microfluidic device, the imaging system comprising: a sensor element configured to generate a storable image of at least a portion of a microchannel; and a plurality of illumination elements disposed with respect to the sensor element and configured to illuminate a portion of the microfluidic chip to be imaged by the sensor element, wherein at least one of the illumination elements comprises an illumination assembly comprising: an LED; a mask disposed in front of the LED and having an opening formed therein so as to control an area illuminated by the illumination assembly; a filter along an optic path of the illumination assembly for controlling the spectral content of light emitted by the illumination assembly, and a lens for imaging an area with light emitted by the illumination assembly, wherein the LED, the mask, the filter, and the lens are aligned along an optic axis of the illumination assembly.