1. An illumination system for imaging a specimen, the system comprising: a motorized stage, in an optical system, for moving the specimen while an image of the specimen is captured; a pulsed light illumination system in the optical system, wherein the pulse light illumination system optically stops motion on the motorized stage while allowing continuous physical movement of the motorized stage and thus the specimen; a stage position detector, associated with the motorized stage, wherein the stage position detector controls firing of the pulsed light illumination system at predetermined positions of the motorized stage; means for eliminating overlapping or missed specimen between images by precisely aligning the motorized stage and a camera, accurately positioning the motorized stage, and synchronizing the camera and the pulsed light illumination system; and means for capturing well aligned image tiles for creation of an image montage.