Dual-axis electron tomography is an important 3xe2x80x89D macro-molecular structure reconstruction technology, which can reduce artifacts and suppress the effect of missing wedge. However, the fully automatic data process for dual-axis electron tomography still remains a challenge due to three difficulties: (i) how to track the mass of fiducial markers automatically, (ii) how to integrate the information from the two different tilt series, and (iii) how to cope with the inconsistency between the two different tilt series.