A three-dimensional (3D) x-ray tomographic imaging system includes an x-ray source fixedly attached to a first unmanned vehicle, which can be aerial or otherwise configured for locomotion, and an x-ray detector. A vehicle controller is configured to be operated by an operator, and an optical camera is mounted to the first unmanned vehicle at a fixed position relative to the x-ray source, and an optical pattern is fixed at a position relative to the x-ray detector. The x-ray source and x-ray detector are configured to be positioned on substantially opposite sides of the object, while the x-ray source is rotated radially around the object to one or more imaging positions.