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Related Concept Videos

Total Internal Reflection Fluorescence Microscopy01:05

Total Internal Reflection Fluorescence Microscopy

Total internal reflection fluorescence microscopy or TIRF is an advanced microscopic technique used to visualize fluorophores in samples close to a solid surface with a higher refractive index, such as a glass coverslip. TIRF only allows fluorophores in proximity to the solid surface to be excited. When light from a medium with a lower refractive index (such as air) hits the glass coverslip at a critical angle, the light undergoes total internal reflection stead of passing through the glass.

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Related Experiment Video

Updated: Jun 4, 2026

Multimodal Optical Microscopy Methods Reveal Polyp Tissue Morphology and Structure in Caribbean Reef Building Corals
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Protocol for quantifying and modeling light scattering in coral microskeletons.

Netanel Kramer1, Steven L Jacques2, Daniel Wangpraseurt1

  • 1Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.

STAR Protocols
|June 2, 2026
PubMed
Summary

This study introduces a new method to measure light scattering in coral skeletons, crucial for understanding coral health and photosynthetic performance. The protocol allows for detailed light propagation analysis in coral ecosystems.

Keywords:
BiophysicsEnvironmental sciencesModel OrganismsStructural Biology

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Last Updated: Jun 4, 2026

Multimodal Optical Microscopy Methods Reveal Polyp Tissue Morphology and Structure in Caribbean Reef Building Corals
10:39

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Physiological Characterization of the Coral Holobiont Using a New Micro-Respirometry Tool
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Physiological Characterization of the Coral Holobiont Using a New Micro-Respirometry Tool

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Area of Science:

  • Marine Biology
  • Optical Physics
  • Ecology

Background:

  • Coral health and photosynthetic performance are significantly influenced by light availability.
  • Skeleton optical properties play a critical role in regulating light penetration within coral tissues.
  • Quantifying light scattering in coral skeletons is essential for ecological research.

Purpose of the Study:

  • To present a non-invasive protocol for quantifying and modeling light scattering in coral microskeletons.
  • To enable high-resolution characterization of light propagation within coral structures.
  • To provide a framework for understanding how coral skeletons affect light availability for photosynthesis.

Main Methods:

  • Developed a protocol to extract scattering coefficients from coral microskeletons.
  • Utilized theoretical models to convert scattering coefficients to inherent optical properties.
  • Employed Monte Carlo photon transport simulations on 3D coral geometries.
  • Calculated fluence distributions across skeleton and water layers.

Main Results:

  • Successfully quantified light scattering properties of coral microskeletons.
  • Modeled photon transport and light distribution within coral structures.
  • Established a method for high-resolution coral light-propagation characterization.

Conclusions:

  • The presented protocol offers a robust method for analyzing light scattering in corals.
  • This approach enhances our understanding of light-dependent processes in coral ecosystems.
  • The findings support ecological research by providing detailed insights into coral optical properties.