Methods, systems, and apparatus, including computer programs encoded on computer-storage media, for a lighting controller for sea lice detection. In some implementations, a pulse of red light and a pulse of blue light can be timed with the exposure of a camera to capture multiple images of a fish or group of fishes in both red and blue light. 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.