The repository contains the datasets and implementation of the method described in: Wang et al., "Automatic labeling of vascular structures with topological constraints via HMM", MICCAI 2017. Please refer to the "ReadMe.txt" file for details of code setup, datasets and results. We propose a novel graph labeling approach to anatomically label vascular structures of interest. Our algorithm can handle different topologies, like circle, chain and tree. By using coordinate independent geometrical features, it does not require prior global alignment.