Final optics of high energy laser facilities are susceptible to laser-induced damage that reduces the quality of laser beams. In such facilities, images of protection windows are acquired on a daily basis. However, some motions may occur in addition to illumination changes. A method based on registration principles is developed to detect and quantify laser damage sites, which leads to sub-pixel resolution and corrects for brightness and contrast variations. The procedure is applied to a set of actual images of a silica window. The proposed approach is efficient to ensure reliable monitoring of damage inception and growth.