Automatic acquisition of fiducial markers and alignment of images in tilt series for electron tomography

Three-dimensional reconstruction of a section of biological tissue by electron tomography requires precise alignment of a series of two-dimensional images of the section made at numerous successive tilt angles. Gold beads on or in the section serve as fiducial markers. A scheme is described that automatically detects the position of these markers and indexes them from image to image. Time resulting set of position vectors are arranged in a matrix representation of the tilt geometry and, by inversion, alignment information is obtained. The scheme is convenient,, requires little operator time and provides an accuracy of <2 pixels RMS, A tilt series of 60-70 images can be aligned in similar to 30 min on any modern desktop computer.