Calibration for plenoptic imaging systems. The calibration preferably is performed automatically by a processor. In one approach, the processor accesses a plenoptic image captured by the plenoptic imaging system. The plenoptic image is analyzed to determine reference points for superpixels of the plenoptic imaging system, for example the centers of the superpixels. The reference points are used to determine a location of each superpixel relative to the detector array.