Mapping the full vascular network in the mouse brain at submicrometer resolution

Mapping the microvascular networks in the brain can lead to significant scientific and clinical insights. We developed a serial sectioning microscopy technique called the Knife-Edge Scanning Microscopy (KESM) to section and image the entire mouse brain at submicrometer resolution. In our effort to map the entire vascular network in the mouse brain, we perfused the vessels with India ink, and used KESM to image the prepared brain. This results in about 1.5 TB of raw image data which poses a serious challenge in terms of analysis. In this paper, we will present our data set, and computational algorithms we developed to trace and analyze morphological properties of the mouse brain vascular network. Since the data is available across the entire brain in full detail (the smallest capillaries can be observed in our data), it enables the comparison of regional differences in morphological properties. We expect our results to provide rich insights to brain and neuroscience researchers.