In this paper we present a new approach to registration and sequencing of microscope images obtained from serial sections of large blood vessels at macroscopic levels of magnification. It is assumed that subsequent section images may be located inadequately in the image series. Translations and rotations of the object of interest can occur. Some images can be also reflected vertically or horizontally. The proposed algorithm is based on the center of gravity estimation and the phase-only correlation (POC) and uses standard image normalization as a preprocessing procedure. The method is fully-automatic and robust to common image distortions. The quality of registration is measured by the mean value of the sum of absolute difference between images. This criterion can be used also for slide images sequencing, when the image acquisition is performed independently for each section. A set of experiments, carried out using sampled microscopic images of a vein section, proves experimentally the effectiveness of the proposed approach.