Optical Clearing with CLARITY
Refractive Index: 1.45 
Clearing Time: Rapid if active CLARITY - Passive CLARITY takes weeks
Type: Hydrogel 
IHC: Compatible with IHC 
FP: Compatible with FP 
Tissue Morphology: Process leaves proteins intact but destroys cellular morphology 
Carcinogenicity: Yes - polyacrylamide
• Whole-body and Whole-Organ Clearing and Imaging Techniques with Single-Cell Resolution: Toward Organism-Level Systems Biology in Mammals
• Light microscopy mapping of connections in the intact brain
• Optimizing probes to image cleared tissue
Because of the complexity of CLARITY and difficulty to execute the technique, Logos Biosystems and LifeCanvas Technologies have developed automated CLARITY devices called X-CLARITY™ and SmartClear II Pro.
While optical clearing and the concept of 3D histology has been around for a long-time, in 2013 researchers from Stanford brought the concept to the forefront with the introduction of the CLARITY approach. With CLARITY, researchers were able to render whole mouse brains transparent and then image them. The director the NIH Dr. Francis Collins remarked that:
"CLARITY is powerful. It will enable researchers to study neurological diseases and disorders, focusing on diseased or damaged structures without losing global perspective. That’s something we’ve never before been able to do in three dimensions."
The CLARITY approach involves embedding a whole tissue in a polyacrylamide hydrogel and pulling an electrical current through the sample to remove the lipids from the cells . This process renders the tissue transparent through removing cellular components with a low refractive index while leaving the proteins, and nucleic acids intact within the hydrogel matrix .
While this approach is elegant in design and has made its way into numerous publications, researchers cite difficulties with executing this complex process. The process leaves the overall structure of tissues intact but completely irreversibly damages the cellular morphology.