A method includes determining calibration factors for calibrating photon-counting detectors of a spectral imaging system by combining a heuristic calibration of the photon-counting detectors and an analytical calibration of the photon-counting detectors and generating a set of photon-counting calibration factors based on the combining of the a heuristic calibration and the analytical calibration. The photon-counting calibration factors, when applied to measured energy-resolved data from the photon-counting detectors of a spectral CT scan of a subject or object, mitigate spectral distortion caused by a radiation intensity profile shaper that filters a radiation beam of the spectral CT scan.