A biological growth plate scanner includes a multi-color illumination system that illuminates a biological growth plate with different illumination colors. A monochromatic image capture device captures images of the biological growth plate during illumination of the growth plate with each of the illumination colors. A processor combines the images to form a composite multi-color image, and/or individual components of the composite image, and analyzes the composite image to produce an analytical result such as a colony count or a presence/absence result. The biological growth plate scanner may include both front and back illumination components. The back illumination component may include a diffuser element disposed under the biological growth plate. The diffuser element receives light from one or more laterally disposed illumination sources, and distributes the light to illuminate a back side of the biological growth plate. The illumination sources in the front and back illumination components may take the form of sets of light emitting diodes (LEDs) that can be independently controlled by the processor.