Methods, systems, and devices are disclosed for charged particle tomography imaging. In one aspect, a system includes a charged particle tomography scanner (CPTS) unit to detect individual charged particles of an emitted charged particle beam delivered to a subject by a charged particle delivery (CPD) system, and a processing unit to determine the angular trajectory change (scattering) and energy loss of the charged particle beam based on detected trajectory information and produce an anatomical image. The CPTS unit includes two detectors, one positioned between the subject and the CPD system, and the other detector positioned opposite to the first detector to detect the trajectory information of the individual charged particles of the charged particle beam having passed through the first detector and the subject, and a motion control unit to move the detectors, in which the detectors' size covers an area at least that of the beam's cross-section.