When calibrating a positron emission tomography (PET) scanner, a radioactive calibration phantom is scanned over a period of several half lives to acquire a plurality of frames of scan data. Interlaced timing windows are employed to facilitate acquiring coincidence data for a plurality of coincidence timing windows and energy windows during a single calibration scan. Coincident events are binned according to each of a plurality of selected coincidence windows, and the PET scanner is calibrated for each of the plurality of coincidence timing windows using data acquired from the single calibration scan.