Visualization and molecular characterization of whole-brain vascular networks with capillary resolution

Nat Commun. 2020 Feb 27;11(1):1104. doi: 10.1038/s41467-020-14786-z.


Structural elucidation and molecular scrutiny of cerebral vasculature is crucial for understanding the functions and diseases of the brain. Here, we introduce SeeNet, a method for near-complete three-dimensional visualization of cerebral vascular networks with high signal-to-noise ratios compatible with molecular phenotyping. SeeNet employs perfusion of a multifunctional crosslinker, vascular casting by temperature-controlled polymerization of hybrid hydrogels, and a bile salt-based tissue-clearing technique optimized for observation of vascular connectivity. SeeNet is capable of whole-brain visualization of molecularly characterized cerebral vasculatures at the single-microvessel level. Moreover, SeeNet reveals a hitherto unidentified vascular pathway bridging cerebral and hippocampal vessels, thus serving as a potential tool to evaluate the connectivity of cerebral vasculature.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bile Acids and Salts / chemistry
  • Brain / blood supply
  • Brain / diagnostic imaging*
  • Brain / pathology
  • Capillaries / diagnostic imaging*
  • Cerebrovascular Circulation*
  • Cross-Linking Reagents / chemistry
  • Fluorescent Dyes / chemistry
  • Histocytological Preparation Techniques / methods*
  • Hydrogels / chemistry
  • Imaging, Three-Dimensional*
  • Luminescent Agents / chemistry
  • Luminescent Proteins / chemistry
  • Luminescent Proteins / genetics
  • Mice
  • Microscopy, Fluorescence / methods
  • Perfusion
  • Polymerization
  • Signal-To-Noise Ratio


  • Bile Acids and Salts
  • Cross-Linking Reagents
  • Fluorescent Dyes
  • Hydrogels
  • Luminescent Agents
  • Luminescent Proteins
  • red fluorescent protein