Methods, systems, and apparatus, including computer programs encoded on computer-storage media, for a lighting controller for sea lice detection. In some implementations, fish are contained within an elliptical tank filled with water. An imaging station located on the elliptical tank is used to capture an image of a fish from which image analysis can be performed to detect sea lice or other skin features, including lesions, on the fish. Pairs of imaging assemblies coordinate pulsing light of at least a first and a second color and capturing images of the fish while the fish is illuminated by at least the first and the second color. By using the captured images with different color light, computers can detect features on the body of a fish including sea lice, skin lesions, shortened operculum or other physical deformities and skin features. Detection results can aid in mitigation techniques or be stored for analytics. For example, sea lice detection results can inform targeted treatments comprised of lasers, fluids, or mechanical devices such as a brush or suction.