Tissue clearing is about refractive index matching, making sure all components of the cells within a tissue have similar refractive indexes so that light can pass through without scattering. There are 3 methods to achieve tissue clearing: 

  1. Protein hyper-hydration: TDE, Scale, SeeDB, CUBIC, Fruit, ClearT, FocusClear 

  2. Solvent high refractive index matching: Visikol, HISTO technology, BABB, i/3/u/vDISCO 

  3. Hydrogel embedding, remove lipids to provide clarity: CLARITY, PACT, PARS, SWITCH 


Abcam provides a comprehensive series of 4 videos that go over the considerations when starting to use tissue clearing techniques 


  • Introduction to different methods for tissue clearing – pros and cons 

  • Optimizing tissue thickness and antibody concentration 

  • Considerations for direct and indirect labeling, auto-fluorescence, and multi-color labeling 

  • Imaging considerations, modality, objective, and refractive index matching.  

A review by Ueda, H.R., 2020 provides a table of reagents used as well as imaging modality considerations.