An apparatus for analyzing a plurality of samples in sample sites on a substrate, the apparatus having an array of spaced apart light sources coupled to a moveable support so that one or more of the light sources can be selectively used; a frame for supporting the substrate; a detector configured to detect light; an optical relay configured to transmit light from at least one of the plurality of light sources to a sample site and from the sample site to the detector; and a support structure for supporting the frame, the detector and the optical relay.