Developing 3D microscopy with CLARITY on human brain tissue: Towards a tool for informing and validating MRI-based histology

Neuroimage. 2018 Nov 15:182:417-428. doi: 10.1016/j.neuroimage.2017.11.060. Epub 2017 Nov 28.


Recent breakthroughs in magnetic resonance imaging (MRI) enabled quantitative relaxometry and diffusion-weighted imaging with sub-millimeter resolution. Combined with biophysical models of MR contrast the emerging methods promise in vivo mapping of cyto- and myelo-architectonics, i.e., in vivo histology using MRI (hMRI) in humans. The hMRI methods require histological reference data for model building and validation. This is currently provided by MRI on post mortem human brain tissue in combination with classical histology on sections. However, this well established approach is limited to qualitative 2D information, while a systematic validation of hMRI requires quantitative 3D information on macroscopic voxels. We present a promising histological method based on optical 3D imaging combined with a tissue clearing method, Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging compatible Tissue hYdrogel (CLARITY), adapted for hMRI validation. Adapting CLARITY to the needs of hMRI is challenging due to poor antibody penetration into large sample volumes and high opacity of aged post mortem human brain tissue. In a pilot experiment we achieved transparency of up to 8 mm-thick and immunohistochemical staining of up to 5 mm-thick post mortem brain tissue by a combination of active and passive clearing, prolonged clearing and staining times. We combined 3D optical imaging of the cleared samples with tailored image processing methods. We demonstrated the feasibility for quantification of neuron density, fiber orientation distribution and cell type classification within a volume with size similar to a typical MRI voxel. The presented combination of MRI, 3D optical microscopy and image processing is a promising tool for validation of MRI-based microstructure estimates.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aged
  • Autopsy
  • Brain* / cytology
  • Brain* / diagnostic imaging
  • Brain* / pathology
  • Female
  • Histological Techniques / methods*
  • Humans
  • Imaging, Three-Dimensional / methods*
  • Immunohistochemistry
  • Magnetic Resonance Imaging / methods*
  • Male
  • Microscopy / methods*
  • Middle Aged
  • Neuroimaging / methods*
  • Staining and Labeling / methods*
  • Tissue Banks*