Simplified method to perform CLARITY imaging

Ekaterina Poguzhelskaya, Dmitry Artamonov, Anastasia Bolshakova, Olga Vlasova, Ilya Bezprozvanny

Research output: Contribution to journalArticlepeer-review

37 Scopus citations


Background: Imaging methods are used widely to understand structure of brain and other biological objects. However, sample penetration by light microscopy is limited due to light scattering by the tissue. A number of methods have been recently developed to solve this problem. In one approach (SeeDB) simple procedure for clarifying brain samples for imaging was described. However, this method is not compatible with immunostaining approach as SeeDB-prepared tissue is not permeable to the antibodies. Another technique for clearing brain tissue (CLARITY) was optimized for immunochemistry, but this method technically much more demanding than SeeDB. Results: Here we report optimized protocol for imaging of brain samples (CLARITY2). We have simplified and shortened the original protocol. Following hydrogel fixation, we cut brain tissue to 1-1.5 mm thick coronal slices. This additional step enabled us to accelerate and simplify clearing, staining and imaging steps when compared to the original protocol. We validated the modified protocol in imaging experiments with brains from line M Thy1-GFP mouse and in immunostaining experiments with antibodies against postsynaptic protein PSD-95 and striatal-specific protein DARPP32. Conclusions: The original CLARITY protocol was optimized and simplified. Application of the modified CLARITY2 protocol could be useful for a broad range of scientists working in neurobiology and developmental biology.

Original languageEnglish (US)
Article number19
JournalMolecular neurodegeneration
Issue number1
StatePublished - May 26 2014


  • 3D brain tissue reconstruction
  • Confocal
  • Neuroimaging
  • Neuronal structure
  • See deep brain
  • Two-photon

ASJC Scopus subject areas

  • Molecular Biology
  • Clinical Neurology
  • Cellular and Molecular Neuroscience


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