Neurodegenerative diseases including Alzheimer’s affect millions around the world, and this number is projected to increase over the years unless a breakthrough is made. There are several theories on the pathogenesis of neurodegenerative diseases, with the amyloid cascade and tau theory being the most prominent ones. The formation of amyloid plaques and tau tangles collapses capillaries in the brain, thereby inducing hypoxia and destruction of neurons from loss of nourishment. While we do understand some of the changes that occur in the brain’s vasculature form the pathogenesis of these diseases, they have not yet been mathematically characterized with precision. A computational pipeline is presented here to analyze optically sectioned mice brain sections imaged via two-photon microscopy and characterize various vasculature parameters which are known to deteriorate from neurogenerative diseases. Our proposed pipeline aims to quantify various brain vasculature parameters, such as, vessel tortuosity, diameter, volume and length, as well the degree of difference to understand disease pathogenesis with the eventual hope of providing drug intervention to regress or minimize these changes.