An example antimicrobial treatment system includes an illumination system configured to deliver illumination that activates a photosensitizing agent applied to a cornea. The system also includes a controller configured to control the illumination system. The controller detects an ulcerative region on a cornea and causes the illumination system to deliver the illumination to activate the photosensitizing agent applied to the ulcerative region according to a set of parameters for treating the ulcerative region. The illumination is restricted to the ulcerative region, and activation of the photosensitizing agent in the ulcerative region generates an antimicrobial effect.