The invention includes methods and apparatus for correcting shading non-uniformity in camera systems. A method includes capturing at least two sets of flatfield images from at least two sets of camera modules under first and second illuminant, respectively. Pixels for each image in the sets of flatfield images are then averaged to form first and second averaged flatfield images, respectively. The first averaged flatfield image is transformed using the second averaged flatfield image to create a transform image. The transform image is then saved in memory for calibrating the shading non-uniformity of the camera module.