DOI: 10.5061/dryad.41ns1rnr9
title: Depth-dependent microskeletal features modify light harvesting in Turbinaria reniformis corals

description: 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.
description: # Depth-Dependent Microskeletal Features Modify Light Harvesting in
 Turbinaria reniformis Corals Dataset DOI:
 [10.5061/dryad.41ns1rnr9](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*** 1. **MC_mesh.m** – Main code. Run Monte
 Carlo light transport simulations on voxelized coral. Calls: 2.
 **makeCoralList.m** – Define optical properties for coral tissues and
 water. 3. **makeCoral.m** – Create tissue structures and parameter files
 for Monte Carlo simulation. 4. **VOXELISE.m** – Convert coral STL mesh
 into a voxel grid. 5. **mcxyz.c** – Simulate light propagation (called by
 MC_mesh.m). 6. **splitCoralLayers.m** – Splits 3D coral mesh into
 top/bottom layers based on height for separate optical analysis. 7.
 **lookmcxyz.m** – Visualizes Monte Carlo simulation results (fluence,
 absorption) from binary MCXYZ output files. ***OCT Calibration &
 Grid*** 1. **OCT_calibration.m** – Calibrate OCT system using reference
 samples. 2. **generate_murhogrid.m** – Generate (μ, ρ) grid for
 interpolation of optical properties. 3. **getmurhoOCT.m** – Used inside
 generate_murhogrid.m to compute μ and ρ. 4. **setgraph.m** – Utility for
 consistent figure formatting (fonts, labels, titles). ***OCT Image
 Analysis*** 1. **loadCoralTiff.m** – Load TIFF coral images and select
 regions of interest (ROI). 2. **lookCoral.m** / **viewTiffStack.m** –
 Visualize and interact with TIFF stacks. 3. **OCT_coral_analysis.m** –
 Analyze OCT images: fit exponential decay, extract μ and ρ. 4.
 **breaking_point.m** – Find optimal breaking points for piecewise fitting
 (called by OCT_coral_analysis.m) 5. **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 area * `p` = polyp area * **n** =
 Sample number * **feature** = Skeletal feature analyzed in the scan: *
 `grooves` = coenosteum grooves * `spines` = coenosteum spines *
 `columella` = columella * `septa` = septa 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