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We presented an automatic method for detecting and tracking colloidal gold fiducial markers for alignment in electron tomography (ET). The second-order derivative of direction was used to detect a fiducial marker accurately. The detection was optimized to be selective to the size of fiducial markers. A preliminary tracking result from the normalized correlation coefficient was refined using the detector. A constraint model considering the relationship among the fiducial markers on different images was developed for removing outlier. The three-dimensional positions of the detected fiducial markers and the projection parameters of tilt images were calculated for post process. The accuracy of detection and tracking results was evaluated from the residues by the software IMOD. Application on transmission electron microscopic images also indicated that the presented method could provide a useful approach to automatic alignment in ET.

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