Cubic Clearing
Cubic Clearing - Related Videos
09:54
Imaging Serotonergic Fibers in the Mouse Spinal Cord Using the CLARITY/CUBIC Technique
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Cited by 13 •
2016
Supraspinal projections are important for pain perception and other behaviors, and serotonergic fibers are one of these fiber systems. The present study focused on the application of the combined CLARITY/CUBIC protocol to the mouse spinal cord in order to investigate the termination of these serotonergic fibers.
07:30
Imaging Cleared Embryonic and Postnatal Hearts at Single-cell Resolution
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Cited by 8 •
2016
We describe a protocol to volumetrically image fluorescent protein labeled cells deep inside intact embryonic and postnatal hearts. Utilizing tissue-clearing methods in combination with whole mount staining, single fluorescent protein-labeled cells inside an embryonic or postnatal heart can be imaged clearly and accurately.
08:09
CUBIC Protocol Visualizes Protein Expression at Single Cell Resolution in Whole Mount Skin Preparations
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Cited by 9 •
2016
This report describes a CUBIC protocol to clarify full thickness mouse skin biopsies, and visualize protein expression patterns, proliferating cells, and sebocytes at the single cell resolution in 3D. This method enables accurate assessment of skin anatomy and pathology, and of abnormal epidermal phenotypes in genetically modified mouse lines.
05:50
CUBIC-based Protein Expression Visualization: A Procedure for Visualizing Protein Expression in Full Thickness Mouse Skin Biopsies
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2023
This video describes the CUBIC-based visualization technique, a tissue clearing-dependent imaging technique for visual assessment of protein expression in whole-mount skin biopsies at single-cell resolution in 3D. This technically simple protocol allows the visualization of skin proteins without preparing skin sections.
04:31
Whole-Kidney Three-Dimensional Staining with CUBIC
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Cited by 5 •
2022
The present protocol describes a tissue clearing method and whole-mount immunofluorescent staining for three-dimensional (3D) kidney imaging. This technique can offer macroscopic perspectives in kidney pathology, leading to new biological discoveries.
FAQs
Amino alcohol-containing reagents drive the chemical delipidation step, reducing the lipid-related optical obstruction that makes intact tissue difficult to image. This treatment is paired with, rather than substituted for, refractive-index matching, so the specimen becomes suitable for three-dimensional visualization while fluorescent signals remain available. The combined chemistry supports analysis of structures distributed through thick organs.
Refractive-index matching reduces optical mismatch within the processed specimen, complementing delipidation. This pairing is important because chemical removal of lipids alone does not describe the complete imaging strategy: CUBIC uses both tissue chemistry and optical adjustment to produce transparent samples. In practice, matching the refractive index helps make the cleared organ suitable for whole-volume three-dimensional imaging.
After the clearing chemistry, antibody staining can label selected cell types across thick specimens. This adds cellular specificity to the transparent volume, allowing an investigator to associate a labeled population with surrounding tissue architecture rather than viewing isolated sections. In developmental studies, that combination can reveal how particular cells are positioned within embryonic organs, neuronal projections, or vascular networks.
A typical workflow starts with chemical delipidation using amino alcohol-containing reagents. The specimen then undergoes refractive-index matching to support optical transparency, followed, when targeted labeling is needed, by antibody staining. Finally, the intact sample is examined by three-dimensional imaging. This sequence links preparation, cell-type labeling, and whole-tissue visualization without requiring physical sectioning.
Cubic Clearing is useful when a research question depends on relationships across an entire embryonic or organ-scale volume. Investigators can examine morphogenetic structures, neuronal projections, and vascular networks in their spatial context, rather than limiting interpretation to selected tissue sections. This makes it possible to connect cellular patterns with whole-tissue architecture during development.
The resulting volumes can support quantitative analysis of developmental organization and direct comparison between normal and experimentally altered specimens. Researchers may evaluate how cellular patterns, morphogenetic structures, neuronal projections, or vascular networks differ across conditions while retaining their spatial relationships. Because imaging occurs without sectioning, interpretation can address whole-tissue architecture rather than reconstructed fragments.