We have developed calibration and data processing techniques optimized specifically for photon-integrating pixel array detectors (PADs). Primary effects to be calibrated are pixel gain variation and pixel area variation. Gain variations originate in pixel electronics and may be corrected for via a multiplicative factor. In contrast, area variations result from doping inhomogeneities in the sensor diode, which induce lateral fields that disturb the path of charge carriers as they traverse the diode, resulting in variation in the area mapped to each pixel, depending on the X-ray energy. Methods for measuring both effects are described. Additionally, the single-photon sensitivity used in the gain calibration enables flexible thresholding of events in low-fluence data. © 2013 IOP Publishing Ltd.