Automatic coarse-alignment for TEM tilt series of rod-shaped specimens collected with a full angular range

An automatic coarse-alignment method for a tilt series of rod-shaped specimen collected with a full angular range (from alpha=-90 degrees to +90 degrees, alpha is the tilt angle of the specimen) is presented; this method is based on a cross-correlation method and uses the outline of the specimen shape. Both the rotational angle of the tilt axis and translational value of each image can be detected in the images without the use of markers. This method is performed on the basis of the assumption that the images taken at alpha=-90 degrees and alpha=+90 degrees are symmetric about the tilt axis. In this study, a carbon rod on which gold particles have been deposited is used as a test specimen for the demonstration. This method can be used as an automatic coarse-alignment method prior to the application of a highly accurate alignment method because the alignment procedure can be performed automatically except for the initial setup of some parameters.