The Laboratory of biological electron microscopy and structural biology

(dr. fei sun’s lab)



We have developed a software package towards automatic electron tomography (ET): Automatic Tomography (AuTom). The presented package has the following characteristics: accurate alignment modules for marker-free datasets containing substantial biological structures; fully automatic alignment modules for datasets with fiducial markers; wide coverage of reconstruction methods including a new iterative method based on the compressed-sensing theory that suppresses the "missing wedge" effect; and multi-platform acceleration solutions that support faster iterative algebraic reconstruction. AuTom aims to achieve fully automatic alignment and reconstruction for electron tomography and has already been successful for a variety of datasets. AuTom also offers user-friendly interface and auxiliary designs for file management and workflow management, in which fiducial marker-based datasets and marker-free datasets are addressed with totally different subprocesses. With all of these features, AuTom can serve as a convenient and effective tool for processing in electron tomography.


Han R., Wan X., Wang Z., Hao Y., Zhang J., Chen Y., Gao X., Liu Z., Ren F., Sun F.*, and Zhang F.* (2017), AuTom: a novel automatic platform for electron tomography reconstruction. Journal of Structural Biology, 199(3): 196-208. doi: 10.1016/j.jsb.2017.07.008. (The program AuTom can be downloaded from

(In collaboration with Prof. Fa Zhang, Institute of Computation Technology, CAS)

AuTom: a novel automatic platform for electron tomography reconstruction

Graphical user interface of AuTom. (a) Project management interface. (b) Work-flow selection page. (c) Parameters of project configuration file. (d) Marker-free alignment page. (e) Reconstruction page.