A system for calibrating a charged particle pencil beam includes a first pixelated detector, a second pixelated detector, a beam stop, and a diagnostics system. The first and second pixelated detectors measure the pencil beam at positions proximal and/or distal to an isocenter plane. The beam stop is configured to detect an energy level of the pencil beam. The diagnostics system is configured to transmit a signal to request a generation of the charged particle pencil beam at different settings. The diagnostics system is also configured to update a calibration parameter for each setting based on the data received from the pixelated detectors and the beam stop.
