Authors: Mohammad Haft-Javaherian, Martin Villiger, Chris B. Schaffer, Nozomi Nishimura, Polina Golland, Brett E. Bouma Description: The clinical evidence suggests that cognitive disorders are associated with vasculature dysfunction and decreased blood flow in the brain. Hence, a functional understanding of the linkage between brain functionality and the vascular network is essential. However, methods to systematically and quantitatively describe and compare structures as complex as brain blood vessels are lacking. 3D imaging modalities such as multiphoton microscopy enables researchers to capture the network of brain vasculature with high spatial resolutions. Nonetheless, image processing and inference are some of the bottlenecks for biomedical research involving imaging, and any advancement in this area impacts many research groups. Here, we propose a topological encoding convolutional neural network based on persistent homology to segment 3D multiphoton images of brain vasculature. We demonstrate that our model outperforms state-of-the-art models in terms of the Dice coefficient and it is comparable in terms of other metrics such as sensitivity. Additionally, the topological characteristics of our model's segmentation results mimic manual ground truth. Our code and model are open source at https://github.com/mhaft/DeepVess.