Systems and methods for calibrating an array camera are disclosed. Systems and methods for calibrating an array camera in accordance with embodiments of this invention include the detecting of defects in the imaging components of the array camera and determining whether the detected defects may be tolerated by image processing algorithms. The calibration process also determines translation information between imaging components in the array camera for use in merging the image data from the various imaging components during image processing. Furthermore, the calibration process may include a process to improve photometric uniformity in the imaging components.