Mapping the Fine-Scale Organization and Plasticity of the Brain Vasculature

The cerebral vasculature is a dense network of arteries, capillaries, and veins. Quantifying variations of the vascular organization across individuals, brain regions, or disease models is challenging. We used immunolabeling and tissue clearing to image the vascular network of adult mouse brains and developed a pipeline to segment terabyte-sized multichannel images from light sheet microscopy, enabling the construction, analysis, and visualization of vascular graphs composed of over 100 million vessel segments. We generated datasets from over 20 mouse brains, with labeled arteries, veins, and capillaries according to their anatomical regions. We characterized the organization of the vascular network across brain regions, highlighting local adaptations and functional correlates. We propose a classification of cortical regions based on the vascular topology. Finally, we analysed brain-wide rearrangements of the vasculature in animal models of congenital deafness and ischemic stroke, revealing that vascular plasticity and remodeling adopt diverging rules in different models. [Display omitted] •TubeMap enables fast construction of labeled vascular graphs from TB-sized images•Automated arterio-venous annotations are based on iDISCO+ immunolabeling•We measure regional variations in vessel topology and arterio-venous distances•We study the plasticity of this network in stroke and sensory-deprivation models TubeMap, a pipeline for characterizing brain-wide variations in vascular topology, including vessel network structure, geometry, and arterio-venous labeling, was developed and used to investigate vascular remodeling in models of ischemic stroke and sensory loss.