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A recent discovery in neuroscience prompts the need for innovation in image analysis. Neuroscientists have discovered the existence of meningeal lymphatic vessels in the brain and have shown their importance in preventing cognitive decline in mouse models of Alzheimer s disease. With age, lymphatic vessels narrow and poorly drain cerebrospinal fluid, leading to plaque accumulation, a marker for Alzheimer s disease. The detection of vessel boundaries and width are performed by hand in current practice and thereby suffer from high error rates and potential observer bias. The existing vessel segmentation methods are dependent on user-defined initialization, which is time-consuming and difficult to achieve in practice due to high amounts of background clutter and noise. This work proposes a level set segmentation method featuring hierarchical matting, LyMPhi, to predetermine foreground and background regions. The level set force field is modulated by the foreground information computed by matting, while also constraining the segmentation contour to be smooth. Segmentation output from this method has a higher overall Dice coefficient and boundary F1-score compared to that of competing algorithms. The algorithms are tested on real and synthetic data generated by our novel shape deformation based approach. LyMPhi is also shown to be more stable under different initial conditions as compared to existing level set segmentation methods. Finally, statistical analysis on manual segmentation is performed to prove the variation and disagreement between three annotators.