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Updated: Jan 25, 2026
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Optical Clearing of the Mouse Central Nervous System Using Passive CLARITY
Published on: June 30, 2016
14.0K
Optical clearing potential of immersion-based agents applied to thick mouse brain sections
Mathew Loren1,2, Christian Crouzet1,2, Adrian Bahani1,2
1Department of Biomedical Engineering, University of California, Irvine, California, United States of America.
Plos One
|May 11, 2019
Summary
Optical clearing agents (OCAs) improve 3D brain tissue visualization. ScaleSQ offered the best clearing but altered sample volume and microvascular density, necessitating a framework for evaluating OCAs.
Area of Science:
- Neuroscience
- Biomedical Optics
- Histology
Background:
- Immersion-based optical clearing agents (OCAs) allow 3D visualization of thick brain sections.
- Previous studies demonstrated OCA efficacy but lacked comparative analysis.
Purpose of the Study:
- To evaluate and compare the performance of different immersion-based OCAs.
- To establish a quantitative framework for OCA screening and characterization.
Main Methods:
- Mouse brain sections were immersed in four different OCAs: FocusClear, RIMS, sRIMS, and ScaleSQ.
- Transparency, volume changes, optical clearing spectrum, reversibility, and imaging depth were assessed.
- Microvascular density was analyzed post-clearing.
Main Results:
- All evaluated OCAs affected tissue transparency and volume.
- Optical clearing effects spanned the visible spectrum and were reversible.
- ScaleSQ demonstrated the highest optical clearing potential and imaging depth enhancement.
- ScaleSQ also induced the largest volume change and decreased apparent microvascular density.
Conclusions:
- A quantitative framework for assessing OCA performance is proposed.
- The choice of OCA involves a trade-off between clearing efficiency and sample integrity.
- This framework aids in optimizing experimental design and cost-benefit analysis for optical clearing techniques.
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