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
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. Due to the complete removal of lipid structures, the CLARITY technique significantly transforms tissue histochemistry and can cause significant alterations in tissue morphology. There have been a number of researchers who report loss of antigenicity and difficulties with employing immunolabeling in conjunction with CLARITY. Active CLARITY (utilizing electrophoretic techniques to drive out lipids and increase rate of processing) has also been shown to induce damage to tissues due to high currents required in processing, a significant risk when dealing with valuable tissue samples.
Want to learn more about tissue clearing? Download our Tissue Clearing Ebook
• 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
• A versatile clearing agent for multi-modal brain imaging
- CLARITY wiki
- Clarity Resource Center
- Clarity Forum
- Chung Lab Resources
- Clearing and Labeling Techniques for Large-Scale Biological Tissues
- A multi modal clearing method for brain imaging
- Making Biology Transparent
- Clearing Procedures for Deep Tissue Imaging
- Viviana Gradinaru Interview: How can advances in tissue clearing and optogenetics contribute to our understanding of normal and diseased biology?