Whole-Brain Vasculature Reconstruction at the Single Capillary Level

Sci Rep. 2018 Aug 22;8(1):12573. doi: 10.1038/s41598-018-30533-3.


The distinct organization of the brain's vascular network ensures that it is adequately supplied with oxygen and nutrients. However, despite this fundamental role, a detailed reconstruction of the brain-wide vasculature at the capillary level remains elusive, due to insufficient image quality using the best available techniques. Here, we demonstrate a novel approach that improves vascular demarcation by combining CLARITY with a vascular staining approach that can fill the entire blood vessel lumen and imaging with light-sheet fluorescence microscopy. This method significantly improves image contrast, particularly in depth, thereby allowing reliable application of automatic segmentation algorithms, which play an increasingly important role in high-throughput imaging of the terabyte-sized datasets now routinely produced. Furthermore, our novel method is compatible with endogenous fluorescence, thus allowing simultaneous investigations of vasculature and genetically targeted neurons. We believe our new method will be valuable for future brain-wide investigations of the capillary network.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Brain / blood supply*
  • Brain / cytology
  • Capillaries / diagnostic imaging*
  • Capillaries / physiology
  • Image Processing, Computer-Assisted*
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Microscopy, Fluorescence*
  • Neovascularization, Physiologic
  • Neurons / cytology
  • Signal-To-Noise Ratio
  • Tomography