Automatically pick fiducial markers in electron tomography tilt images

In electron microscope tomography, the alignment of tilt series images is a major determining factor of resolution in the 3D reconstruction. One method of tilt alignment uses gold beads deposited on or in the specimen as the fiducial markers. This paper describes an "auto pick" software system which can pick markers automatically. It uses a cross correlation function to find out the shift between tilts, predicts markers position, refines them in a local search area, detects and corrects wrongly picked markers automatically. The automatically picked result has a comparable accuracy to the manually picked result in our data set used to check this "auto pick" system.