In one aspect, a charged particle tomography and radiation therapy system includes a charged particle tomography scanner (CPTS) unit to detect at least some of the charged particles of an emitted charged particle beam delivered to a region of interest of a subject. A processing unit can determine energy loss of the charged particle beam based on the detected trajectory information. An incoming detector is positioned to detect trajectory information of the at least some of the charged particles entering the subject. An outgoing detector is positioned to detect trajectory information of the at least some of the charged particles passing through and exiting the subject. A motion control unit can control movement of the incoming and outgoing detectors. The incoming and outgoing detectors are sized to cover at least an area substantially equivalent to the beam's cross-section. The processing unit can map radiation dose of the region of interest.