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Micro-computed tomography is an advanced tool for observing three-dimensional tissue structures with high densities. It has been widely used to study the various vascular patterns. In this paper, a novel image analysis procedure based on micro-computed tomography is proposed for the quantification of vessel morphology. The quantification is obtained by first extracting the vessels, collecting their topological information and then calculating the geometric characteristics of the vessels. The methods of measuring vessel density, diameter and tortuosity are given in this paper. The accuracy and precision of the algorithm are evaluated through data from cerebral angiography. The result shows its great potential for future application.