Image sensors have photodiodes separated by isolations regions formed from p-well or n-well implants. Isolation regions may be formed that are narrow and deep. Isolation regions may be formed in a multi-step process that selectively places implants at desired depths in a substrate. Complementary photoresist patterns may be used. To form an implant near the surface of a substrate, a photoresist pattern with openings over the desired implant area may be used. Subsequent implantation may use a complementary pattern such that ions pass through photoresist before implanting in desired regions of a substrate.