The Laboratory of biological electron microscopy and structural biology

(dr. fei sun’s lab)



Although the topic of fiducial marker-based alignment in electron tomography (ET) has been widely discussed for decades, alignment without human intervention remains a difficult problem. Specifically, the emergence of subtomogram averaging has increased the demand for batch processing during tomographic reconstruction; fully automatic fiducial marker-based alignment is the main technique in this process. However, the lack of an accurate method for detecting and tracking fiducial markers precludes fully automatic alignment. In this paper, we present a novel, fully automatic alignment scheme for ET. Our scheme has two main contributions: First, we present a series of algorithms to ensure a high recognition rate and precise localization during the detection of fiducial markers. Our proposed solution reduces fiducial marker detection to a sampling and classification problem and further introduces an algorithm to solve the parameter dependence of marker diameter and marker number. Second, we propose a novel algorithm to solve the tracking of fiducial markers by reducing the tracking problem to an incomplete point set registration problem. Because a global optimization of a point set registration occurs, the result of our tracking is independent of the initial image position in the tilt series, allowing for the robust tracking of fiducial markers without pre-alignment. The experimental results indicate that our method can achieve an accurate tracking, almost identical to the current best one in IMOD with half automatic scheme. Furthermore, our scheme is fully automatic, depends on fewer parameters (only requires a gross value of the marker diameter) and does not require any manual interaction, providing the possibility of automatic batch processing of electron tomographic reconstruction.


Han R., Wang L., Liu Z., Sun F.* and Zhang F.* (2015), A novel fully automatic scheme for fiducial marker-based alignment in electron tomography. Journal of Structural Biology 192: 403-17. doi: 10.1016/j.jsb.2015.09.022. 

The program MarkerAuto can be downloaded from Alternatively, the version 1.5.1 of MarkerAuto can also be obtained here.

Version 1.5.1

(In this version, two programs markererase and autogeom were added. Markererase is used to erase gold beads from the original micrographs. And autogeom is used to estimate the geometry of the section, e.g. pitch angle and thickness.)

markerauto_v1.5.1.tar.gz (static lib linked and compatible for most linux systems)

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

A novel fully automatic scheme for fiducial marker-based alignment in electron tomography

Successful detection and tracking of gold beads from the tilt series of micrographs. (a) and (b) The plastic embedded specimen with (a) for the low tilt and (b) for the high tilt. (c) and (d) Cryo-vitrified specimen (KHL) with (c) for the low tilt and (d) for the high tilt.