Methods and systems for setting up inspection of a specimen are provided. One system includes one or more computer subsystems configured for acquiring a reference image for a specimen and modifying the reference image to fit the reference image to a design grid thereby generating a golden grid image. The one or more computer subsystems are also configured for storing the golden grid image for use in inspection of the specimen. The inspection includes aligning a test image of the specimen generated from output of an inspection subsystem to the golden grid image.