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Recent developments in detectors and electronics enable both positron emission tomography (PET) and X-ray computed tomography (CT) data to be acquired concurrently using the same detection front-end for dual-modality PET/CT imaging. Moreover, it would potentially allow substantial reduction of cost and housing size, in addition to facilitating image fusion. However, the lower energy signals ( ~60 keV versus 511 keV) and higher photon flux per pixel ( > 1 Mcps versus 10 kcps) in CT relative to PET cause significant pile-up and dead-time in CT data acquired in photon counting mode. A digital signal processing method was developed and implemented to improve processing of detector signals sampled at low frequency (~ 45 MHz) in presence of pile-up. The method consists in digitally subtracting the detector impulse response at the output of the preamplifier to restore the signal baseline for more accurate energy estimation. When compared to a fixed threshold counting technique, the proposed method features better noise immunity, higher energy resolution and 50% higher rates measured at an estimated true rate of 2.75 Mcps, making CT integration within modern digital PET hardware feasible.