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True 3D Analysis in 3D Unlocks the Black Box of a Tissue to reveal the biological complexity

The Problem with 2D

Current gold standard techniques are over 100 years old and rely on the analysis of 2D thin section FFPE (~5-10 micron). Spatial and morphological analysis of the tissue microenvironment is highly limited as well as limitations with processing hundreds of slides. Therefore, researchers rely on a small sampling of the tissue to understand complex biological processes.

Cancer doesn’t limit itself to 2 dimensions.

Current technologies utilized for preclinical, diagnostic, prognostic, and predictive clinical cancer research are dependent upon two-dimensional (2D) analysis of formalin- fixed paraffin embedded (FFPE) tissue sections (5–10μm).[1]

It has become clear that the heterogeneity within the tumor microenvironment (TME) contributes significantly to the development and eventual metastasis of cancer, as well as the response and resistance to treatment.[2]

3D volumetric image of breast tissue XZ axis

Moving Beyond Slices and Slides

What was science fiction a few years ago is today a reality: It is now possible to trace the path of a single nerve projection through a forest of other cells; Illuminate your tissue microenvironment in a 3D volume; See more biology in 3D; Process samples multiple times using new biomarkers without destroying the tissue; Automate this process and integrate it into your normal tissue processing work flow; Add digital spatial image analysis in 3D to facilitate pre-clinical and clinical research studies. The future has arrived.

The Solution

See More Biology
in True 3D

Researchers need to see more to explore further.  Seeing whole-volume high-content imaging lets context into the tissue analysis phase. If drug discovery and research were a maze of dark paths ahead of you, this would be your flashlight, showing the path ahead and letting you avoid dead ends and see further.

Clarity Tissue Clearing Process from ClearLight


CLARITY is an acronym for
Imaging / Immunostaining / in situ-hybridization-compatible

CLARITY Method Overview

CLARITY: The tissue is embedded in a hydrogel solution of monomers and cross-linkers

Tissues are embedded in a hydrogel matrix to create a mesh

Lipids are cleared to create an optically
transparent hybrid

Resultant hybrid is transparent to light and permeable to molecules

Molecular markers are added to highlight specific features

Cleared Tissue Sample with CLARITY method 5mm dia x 1_1200x

This is nondestructive processing and can be repeated multiple times

Image using Confocal, Light Sheet, Selective Plane Illumination Microscopy (SPIM)

3D volumetric image of breast tissue XZ axis

The ClearLight Difference

Our imaging and informatics capabilities go far beyond immunostaining and tissue clearing. Our in-house proprietary AI and Machine-Learning processes aid in segmentation and classification of the sample at unprecedented detail.

ClearLight Biotechnologies

  • Uses full volumetric imaging
  • Complete spatial analysis in context
  • Reveals relationships and how cells and stains relate to each other.
  • High content imaging
  • Obtaining high-resolution information while maintaining a global perspective

An Overview of the ClearLight Biotechnologies Proprietary 3D Software Workflow

Raw Data




Tissue Analysis and Data from ClearLight Biotechnologies 2

True 3D: The Next Dimension in Tissue Analysis

Disease is one thing that connects all of us, sadly. Every person reading this, others in the room, and the room beyond that, and the all rooms in all the cities, worldwide. Disease connects us all; it also destroys lives and reduces human potential. Thankfully researchers like you are involved in drug discovery and development.

If your research work will benefit from non-destructive tissue processing and True 3D image analysis let’s work together on new possibilities.

Call (408) 329-7769

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: