An apparatus for imaging an array of a plurality of features associated with a sample tile. The apparatus includes a stage that supports the sample tile in an illumination region, and an illumination source having a plurality of LEDs adapted to emit light. At least a portion of the light illuminates the illumination region. Additionally, the apparatus includes an image collecting device adapted to selectively collect images of either a first signal when the illumination source is illuminating the illumination region, or a second signal absent illumination of the illumination region. The first signal has wavelengths effectively different from the wavelengths of the portion of the light emitted by the LEDs that illuminates the illumination region.