Optical Clearing
Optical Clearing - Related Videos
10:28
Optical Clearing of the Mouse Central Nervous System Using Passive CLARITY
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Cited by 11 •
2016
Optical clearing techniques are revolutionizing the way tissues are visualized. In this report we describe modifications of the original Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging-compatible Tissue-hYdrogel (CLARITY) protocol that yields more consistent and less expensive results.
07:15
Transient Optical Clearing Using Absorbing Molecules for Ex Vivo and In Vivo Imaging
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Cited by 1 •
2025
Optical clearing techniques, such as absorbing molecules solutions, reduce light scattering temporarily to enhance biological imaging and offer biocompatible, reversible in vivo imaging strategies for deeply embedded organs. This protocol presents detailed experimental procedures as well as advanced image processing to achieve high-quality, dynamic imaging for real-time dynamics in living animals.
06:18
Optical Clearing and Imaging of Immunolabeled Kidney Tissue
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Cited by 7 •
2019
The combination of antibody labeling, optical clearing, and advanced light microscopy allows three-dimensional analysis of complete structures or organs. Described here is a simple method to combine immunolabeling of thick kidney slices, optical clearing with ethyl cinnamate, and confocal imaging that enables visualization and quantification of three-dimensional kidney structures.
04:55
Optical Clearing of Plant Tissues for Fluorescence Imaging
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Cited by 6 •
2022
Here, a method is described for making plant tissues transparent while maintaining the stability of fluorescent proteins. This technique facilitates deep imaging of cleared plant tissues without physical sectioning.
08:12
Rapid Optical Clearing for Semi-High-Throughput Analysis of Tumor Spheroids
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Cited by 2 •
2022
Tumor spheroids are becoming increasingly utilized to assess tumor cell-microenvironment interactions and therapy response. The present protocol describes a robust but simple method for semi-high-throughput imaging of 3D tumor spheroids using rapid optical clearing.
FAQs
Optical clearing reduces scattering by addressing the chemical sources of optical heterogeneity within tissue. Treatments may remove pigments and lipids, or bring the refractive indices of different tissue components closer together. These changes reduce differences in how light travels through the specimen, allowing illumination and emitted signals to pass more effectively during three-dimensional imaging.
Refractive-index matching makes neighboring tissue components optically more similar, reducing abrupt interfaces that scatter light. This is especially important in thick specimens, where repeated scattering can obscure structures deep inside the sample. By improving optical uniformity, the approach supports clearer visualization of distributed neural features rather than restricting observation to near-surface regions.
Pigment and lipid removal changes the tissue composition by eliminating components that contribute to optical obstruction, whereas refractive-index matching changes how existing components interact with light. Both strategies reduce optical heterogeneity, but they do so through different mechanisms. Chemical treatments can therefore be selected or combined according to the tissue features that limit imaging clarity.
A general workflow begins with chemical treatment of the biological specimen to reduce scattering through pigment or lipid removal, refractive-index matching, or both. Structural features are then preserved while the sample is prepared for labeling and microscopy. Cleared brain or spinal cord tissue can subsequently be examined with light-sheet or confocal imaging to generate three-dimensional anatomical information.
Light-sheet and confocal microscopy are identified as compatible imaging approaches for cleared neural specimens. These methods can support three-dimensional examination of labeled neurons, axonal pathways, vasculature, and broader cellular organization. The resulting images allow investigators to analyze structures throughout a thick brain or spinal cord sample rather than interpreting anatomy from limited two-dimensional sections.
In neuroscience, cleared brain and spinal cord samples support circuit tracing and whole-tissue analysis. Researchers can relate microscopic architecture to neural function by mapping neuronal arrangements, axonal connections, vascular structures, and cellular organization in three dimensions. The same strategy also helps examine disease-related changes, connecting altered tissue anatomy with broader patterns across an intact specimen.