Thy1-YFP mouse brain slices cleared with the X-CLARITY systems and reagents. Thy1-YFP (green), Anti-Collagen IV (red), TO-PRO-3 (blue).


Accelerate Your 3D Imaging Workflow

Tissue clearing is essential for non-destructive, three-dimensional (3D) imaging of biological samples. Combined with labeling techniques, tissue clearing allows for the visualization of cellular structures in their physiological context.

X-CLARITY™ systems and reagents standardize, simplify, and accelerate each step of the tissue clearing process. X-CLARITY™ is based on CLARITY (Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging / Immunostaining /in situ-hybridization-compatible Tissue hYdrogel), a tissue clearing method developed by the Deisseroth lab at Stanford University.

The new DeepLabel™ Antibody Staining Kit accelerates immunolabeling of cleared tissues for a broad range of applications.

Mouse kidney cleared with the X-CLARITY

Standardize & Simplify Each Step

Step1. Tissue Clearing

A fixed tissue sample is incubated in the X-CLARITY™ Hydrogel Solution Kit to allow hydrogel monomers to diffuse uniformly throughout the sample and then placed in the X-CLARITY™ Polymerization System.

Monomers polymerize in the anaerobic environment, linking the biomolecules to a sturdy hydrogel network, preserving molecular information and structural integrity.

The tissue-hydrogel hybrid is cleared in the X-CLARITY™ Tissue Clearing System II using the ready-to-use Electrophoretic Tissue Clearing Solution. Lipids are extracted actively through electrophoresis or passively, leaving behind a stable and transparent tissue-hydrogel hybrid that is chemically accessible for molecular phenotyping.

Step 2. Antibody Labeling.

The transparent sample is then labled with antibodies using the DeepLabel™ Antibody Staining Kit, which enhances antibody penetration into clarified tissues. Optimized for clarified tissue samples, DeepLabel™ can be used with tissues cleared with various clearing methods such as passive or active CLARITY, iDISCO, 3DISCO, uDISCO, Visikol, or CUBIC.


Step 3. RI Matching for Imaging

Prior to imaging, the tissue-hydrogel hybrid is placed in a refractive index (RI) matching solution in order to homogenize the environment within the tissue to the solution. This reduces light scatter, which in turn increases optical transparency and consequently increases image quality and imaging depth.



Mouse brain cleared with the X-CLARITY

X-CLARITY Tissue Processing

  • Simple protocol and ready-to-use reagents
  • Adaptable for various tissue types and applications
  • Long-term preservation of endogenous FP
  • Efficient and homogenous antibody labeling


Mouse lungs and trachea, mouse heart and mouse embryo (E 21.5) cleared with the X-CLARITY, Courtesy of Michal Shoshkes-Carmel, PhD and Andrea Stout, PhD, University of Pennsylvania.


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Webcast: Doug Richardson, Harvard University: The Basic Principles of Clearing and Imaging Biological Tissues

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X-CLARITY in the literature



For research use only. Not for use in diagnostic procedures.



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