Semi-automatically aligned tilt images in electron tomography

In electron microscope tomography, alignment of tilt series images is a major determinant of resolution in 3D reconstructions. One alignment method uses gold beads deposited on or in the specimen as fiducial markers. We have developed software to semi-automatically align tilt series images. It runs two processes iteratively: (1) Marker picking. In this process, it uses a cross-correlation function to determine the shift between tilt images and predicts marker coordinates. Subsequently it refines them in a local search area, and detects and corrects erroneously picked markers automatically. The coordinates of the picked markers are used to align the images. (2) Image alignment. In this process, it uses a least squares method to estimate image rotation, image shift, and image scale factor.