A novel proton imaging system incorporates positron emission detections to enhance proton therapy treatment preparation and procedural efficiencies while reducing operational costs associated with proton therapy. In one case, the novel proton imaging system incorporating a positron emission tomography (PET) module enables rapid on-the-fly in vivo range verification for proton therapy using position information from short-lived positron emitters produced during treatment. This unique in vivo range verification method produces more streamlined, accurate, and cost-effective results relative to conventional proton imaging systems. In another case, the novel proton imaging system incorporating the PET module provides a unique combinatory PET/pCT (proton computer tomography) scanning that creates more accurate maps for proton therapy planning for metabolically-active tumors. This proton imaging system also utilizes a novel concept of “virtual protons” originating from in vivo range verification measurements that mimic proton particle's characteristics for more accurate proton computer tomography (pCT) or computer tomography (CT).