Phenotyping Intact Mouse Bones Using Bone CLARITY

  • Jennifer B. Treweek
  • Aidan Beres
  • Nathan Johnson
  • Alon GreenbaumEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2230)


The bone is typically studied using traditional histology techniques, that is, serial sectioning and staining. While effective, these techniques are laborious and destructive, as the native 3D environment of the bone is not maintained. Presented here is a bone-clearing methodology, termed Bone CLARITY, which combines published techniques for clearing soft tissues, including delipidation for the removal of light-scattering membranes, hydrogel-embedding for the stabilization of fragile epitopes, heme elution for the reduction of blood-based autofluorescence; as well as specialized steps, including decalcification and progressive refractive index matching, for addressing the unique challenges posed by osseous tissue. This method renders the bone transparent and enables the detailed visualization of an intact tissue specimen at multiple spatial scales.

Key words

Tissue Clearing Bone CLARITY Three-dimensional imaging Light-sheet microscopy Fluorescence microscopy 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2021

Authors and Affiliations

  • Jennifer B. Treweek
    • 1
  • Aidan Beres
    • 2
  • Nathan Johnson
    • 2
  • Alon Greenbaum
    • 2
    • 3
    • 4
    Email author
  1. 1.Department of Biomedical EngineeringUniversity of Southern CaliforniaLos AngelesUSA
  2. 2.Joint Department of Biomedical EngineeringNorth Carolina State University and University of North Carolina at Chapel HillRaleighUSA
  3. 3.Comparative Medicine InstituteNorth Carolina State UniversityRaleighUSA
  4. 4.Bioinformatics Research CenterNorth Carolina State UniversityRaleighUSA

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