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Tissue Clearing Applications

CLARITY Beyond the Brain

Evaluation of Normal and Diseased Tissues


Applications of Tissue
Clearing Beyond the Brain

Tissue clearing methods exist to allow for deep tissue imaging. There has been a long history of tissue clearing with many advancements designed to promote particular applications. Of the three main tissue clearing techniques, solvent-based, aqueous-based, and hydrogel embedded, ClearLight has developed expertise in the latter, in particular using the CLARITY protocol. ClearLight has broadened the applicability of the CLARITY method to a wide range of tissues—from the brain to bone.

Normal and Diseased Tissues

We've worked with several biological samples of varying lipidity and complexity and increased our ability to visualize cellular and subcellular structure giving researchers the ability to See More Biology. Chances are, ClearLight has worked with the tissue types useful to your research. ClearLight has evaluated numerous normal and diseased tissues. Our scientists continue to push the envelope of tissue clearing applications.

A Note About Confidentiality

Clients who work with us know that we treat their precious samples, images and videos, and data with the utmost respect and confidentiality. In some cases where we have applied CLARITY to a particular tissue type, we are unable to show specific images or videos. Sometimes this is due to an ongoing study or forthcoming publication. In these cases, we still wish for preclinical researchers to understand that we have applied the CLARITY protocol to a particular tissue type. In those cases, we show a generic icon. Know that when you work with our Lab Services we will treat your precious samples and data with confidentiality, too.

Brain Tissue

CLARITY was the first technique to allow researchers to examine brain structures without disassembling them.

Lung and Lymph Nodes

ClearLight has applied CLARITY to lung carcinomas, healthy lung, and associated lymph nodes.

Skin Samples

The largest organ in the body reveals complex structures when cleared, immunolabeled, and 3D imaged.

Calcified Tissues

Calcified tissues present their own set of challenges. When you work with us you gain the benefit of our internal experiments with bone and teeth.

Kidney Tissue

By clearing whole adult mouse kidneys and imaging in 3D, researchers can gain new insights into kidney structure and function.

Human Tonsil

ClearLight has studied the tonsil using the CLARITY method and analyzed using proprietary AI-based software on 3D volumes of tissue.

Breast Cancer

ClearLight has extensive expertise in three-dimensional imaging and quantitative analysis of CLARITY processed breast cancer tissues.

Human Pancreas

We image intact organs to visualize the tissue and tumor microenvironment without reliance on sectioning and image reconstruction.


ClearLight has applied CLARITY to a range of organoids. This area holds much promise for understanding drug responses and disease models.


ClearLight can clear and stain eyes while retaining their shape and internal structures for 3-dimensional analysis.

Applicable Tissues for Kit Type
High Lipid Kit Low Lipid Kit
Embryo Lung Tissue
Brain Tissue Kidney Tissue
Lymph Nodes Skin Samples
Calcified Tissues (Bone) Cancer (Breast, Lung, etc)
Tonsil Pancreas
Organoids Liver
Eye Intestine
Cell Pellet Muscle
Spinal Cord Heart

Other Tissue Clearing Applications

CLARITY Tissue Clearing is still a relatively new science and there’s so much left to discover. Collaborate with ClearLight to find out how far we can take CLARITY tissue clearing, 3D IHC, and novel use and unique applications for CLARITY tissue cleared samples.

Don't See Your Tissue or Biomarker?

If you require tissue processing for a tissue not shown above a feasibility study may be the next step. We may need to perform antibody feasibility and optimization. We're happy to test your preferred commercial antibody for CLARITY compatibility.

 Collaborative Research Organization for Tissue Clearing Tonsil and Tru3D Tissue Analysis

Leverage our Internal R & D

When you work with us you gain the benefit of our internal experiments, assessments, and rigorous testing. In addition to performing our lab services: CLARITY Tissue Clearing, 3D IHC, and Tru3D Tissue Analysis, ClearLight scientists perform internal Research and Development to advance our understanding and applications of CLARITY to other tissue types and downstream applications. Researchers who work with us benefit from this exploratory work. The ClearLight “lab basement” is full of failed or pivoted experiments that helped inform our path to arrive at what does work. Work with us to avoid making the same mistakes that we have made or going down the blind alleys that we’ve pivoted away from.

“If you don’t want to spend the time figuring it out, we can help. We work hard to make this look easy.” - Dr. Sharla White, VP of Research and Development

Ready to Discuss Your Research Question? Meet with our Application Scientist.



We currently perform non-destructive tissue processing to facilitate pre-clinical research studies.

See Sample Requirements on the Services page. We may support situations not shown. Start a conversation with us using the Contact Us form, email, call (408) 329-7769 or chat with us online.


The value of tissue clearing comes from utilizing samples that are thick enough to be affected by light-scatter, so usually they would be more than 200 microns in thickness. That being said, we have done some work with other samples that have come very close to the lower end of that thickness and have good success in applying our technology. We recommend a brief chat with our Science Team to assess your fit if you are still unsure.

CLARITY Protocol Primer

Visit the CLARITY tissue clearing page to learn the background and specific steps in the CLARITY Tissue Clearing process and to better understand the tissue processing workflow.

ClearLight Lab Services

ClearLight Biotechnologies lab services include tissue clearing using the CLARITY method, 3D immunostaining, 3D imaging (multiplexed fluorescence), and Tru3D tissue analysis.

Optimized Antibodies

ClearLight has many optimized antibodies ready to use with CLARITY and 3D IHC to move your research forward. A feasibility study for new antibodies is available.

Reagent Kits for Tissue Clearing Applications

CLARITY Tissue Clearing Kit – Low Lipid

CLARITY Tissue Clearing Kit – High Lipid

Analysis can be performed for select biomarkers, please contact us to find out if your target of interest is one of them. Imaging is currently performed on select fields of view instead of the entire sample.

Submission Guidelines

Tissue Sample Requirements: