A spectral X-ray imaging system (100) includes an X-ray source (110) and an X-ray detector (120) that are mounted to a support structure (150). The support structure (150) is configured to rotate the X-ray source (110) and the X-ray detector (120) around two or more orthogonal axes (A - A’, B - B’). One or more processors (130) are configured to cause the system (100) to perform operations that include: generating a spectral image based on the spectral image data; and identifying, in the spectral image, a position of a first fiducial marker (180i) comprising a first material, based on a first X-ray absorption k-edge energy value (190i) of the first material.