Depth-dependent microskeletal features modify light harvesting in Turbinaria reniformis corals
Data files
Jul 11, 2025 version files 3.94 GB
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MATLAB_codes.zip
100.17 KB
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OCT_calibration.zip
30.06 MB
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OCT_coral_samples.zip
675.42 MB
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README.md
4.51 KB
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STL_files.zip
3.24 GB
Abstract
Coral skeletal morphology plays a crucial role in modulating light exposure in symbiotic algae, thereby influencing photosynthetic performance and overall energy acquisition. This function is particularly important in environments with limited light availability, such as in mesophotic and deep-water reefs. However, quantifying light capture and distribution within complex coral structures remains challenging. Using optical coherence tomography and high-resolution X-ray scanning, we explored the depth-dependent bio-optical properties of Turbinaria reniformis from shallow and mesophotic environments in the Gulf of Eilat/Aqaba, Red Sea. Our results reveal distinct skeletal layers: a highly scattering superficial layer (~100 μm thick) and a deeper, more light-penetrating layer. Mesophotic corals exhibited a higher scattering coefficient and lower anisotropy of scatter, yielding increased reflectivity, thereby optimizing light use under low-light conditions. Structural features played distinct optical roles: coenosteum grooves facilitated forward scattering and light trapping, while protruding features such as spines and septa increased surface reflectivity and distributed light more broadly. Light simulations further demonstrated an enhanced fluence rate at the skeleton-water interface, with mesophotic corals amplifying the available light up to 2.7-fold. These findings reveal previously unrecognized depth-dependent adaptations that enhance coral light-harvesting efficiency, providing insights into how skeletal morphology supports coral survival across varying light environments.
Dataset DOI: 10.5061/dryad.41ns1rnr9
Description of the data and file structure
MATLAB_codes.zip -
contains the code files used for OCT calibration, sample analysis and Monte Carlo Simulations use in MATLAB software:
Pre-processing & Model Setup For Monte Carlo Simulations
- MC_mesh.m – Main code. Run Monte Carlo light transport simulations on voxelized coral. Calls:
- makeCoralList.m – Define optical properties for coral tissues and water.
- makeCoral.m – Create tissue structures and parameter files for Monte Carlo simulation.
- VOXELISE.m – Convert coral STL mesh into a voxel grid.
- mcxyz.c – Simulate light propagation (called by MC_mesh.m).
- splitCoralLayers.m – Splits 3D coral mesh into top/bottom layers based on height for separate optical analysis.
- lookmcxyz.m – Visualizes Monte Carlo simulation results (fluence, absorption) from binary MCXYZ output files.
OCT Calibration & Grid
- OCT_calibration.m – Calibrate OCT system using reference samples.
- generate_murhogrid.m – Generate (μ, ρ) grid for interpolation of optical properties.
- getmurhoOCT.m – Used inside generate_murhogrid.m to compute μ and ρ.
- setgraph.m – Utility for consistent figure formatting (fonts, labels, titles).
OCT Image Analysis
- loadCoralTiff.m – Load TIFF coral images and select regions of interest (ROI).
- lookCoral.m / viewTiffStack.m – Visualize and interact with TIFF stacks.
- OCT_coral_analysis.m – Analyze OCT images: fit exponential decay, extract μ and ρ.
- breaking_point.m – Find optimal breaking points for piecewise fitting (called by OCT_coral_analysis.m)
- OCT_3D_SA.m – Processes 3D OCT TIFF stacks to calculate surface area using triangulation and extracts boundary lengths.
OCT_calibration.zip -
contains OCT scans (tiff file format) of known reference interfaces use in the program OCT_calibration.m (use MATLAB to open this files):
- 1pss.tiff - 5pss.tiff - Polystyrene microspheres (100 nm) at different concentration (100%, 50%, 25%, 12.5%, 6.25%)
- air 1.0.tiff - air-glass interface scan
- water 1.0.tiff - water-glass interface scan
- oil 1.0.tiff - mineral oil-glass interface scan
- floor noise.tiff – Background noise scan acquired with no sample in OCT field of view.
OCT_coral_samples.zip -
OCT scans (.tiff) of Turbinaria renifromis skeletons from shallow and mesophotic depths, focusing on four different features: columella, septa, coenosteum spines and coenosteum grooves (use MATLAB to open this files).
File naming convention:
Xn_feature.tiff
- Where:
- X = Region of interest on skeleton:
c
= coenosarc areap
= polyp area
- n = Sample number
- feature = Skeletal feature analyzed in the scan:
grooves
= coenosteum groovesspines
= coenosteum spinescolumella
= columellasepta
= septa
- X = Region of interest on skeleton:
Contents:
TD1.zip - TD5.zip - Contains OCT 29 scans (.tiff format) for each sample of shallow Turbinaria renifromis
TD1.zip - TD5.zip - Contains OCT 29 scans (.tiff format) for each sample of mesophotic Turbinaria renifromis
STL_files.zip -
STL 3D models derived from µCT scannings of Turbinaria renifromis skeletons from shallow and mesophotic depths:
TS1.stl - TS5.stl - 3D skeletal scans of shallow *Turbinaria renifromis *
TD1.stl - TD5.stl - 3D skeletal scans of mesophotic *Turbinaria renifromis *
Files and variables
File: MATLAB_codes.zip
Description: contains the codes used for OCT calibration, sample analysis and Monte Carlo Simulations
File: OCT_coral_samples.zip
Description: OCT scans of Turbinaria renifromis skeletons from shallow and mesophotic depths, focusing on four different features: columella, septa, coenosteum spines and coenosteum grooves
File: OCT_calibration.zip
Description: contains OCT scans of known reference interfaces
File: STL_files.zip
Description: STL 3D models derived from µCT scannings of Turbinaria renifromis skeletons from shallow and mesophotic depths
Code/software
MATLAB
Access information
Data was derived from the following sources:
- GAN311 -Ganmede Optical Coherence Tomography (OCT) unit, 930nm, 5.5µm resolution