Code and data for: "Protocol for quantifying and modeling light scattering in coral microskeletons"

This dataset contains MATLAB and C source code used to calibrate Optical Coherence Tomography (OCT) measurements, extract depth-resolved optical properties of coral skeletons, and simulate light transport using voxel-based Monte Carlo models. The workflows summarised here link calibrated OCT reflectance profiles to attenuation and backscatter parameters, which are subsequently mapped onto three-dimensional coral geometries for radiative transfer simulations. Together, these scripts enable reproducible quantification of coral skeletal optical properties and their implications for internal light fields. quick_start_guide.pdf This document provides a visual walkthrough of the pipeline, including direct download links, screenshots, and example outputs. OCT calibration and preprocessing OCT_calibration.mPerforms OCT system calibration using reference interfaces to derive the linear conversion between OCT signal and reflectance. calcMiePSsphere.mUses Mie theory to calculate theoretical scattering parameters for polystyrene spheres used in system calibration. OCT_background_noise.mEstimates the OCT noise floor from signal regions outside the focal volume. OCT data loading and optical parameter extraction OCT_coral_area.m Main analysis scripts that load OCT coral images, extract axial reflectance profiles, fit exponential decay slopes, and compute attenuation (μ) and backscatter (ρ). loadCoralTiff.mLoads OCT TIFF stacks and enables interactive selection of regions of interest. viewTiffStack.mDisplays multi-page OCT TIFF files and allows interactive slice navigation and point selection. lookCoral.mVisualizes OCT-derived optical profiles and fitted results for quality control. breaking_point.mIdentifies depth-dependent breakpoints for multi-slope exponential fitting. getlogscale.mGenerates logarithmically spaced vectors required for creating high-resolution optical lookup grids. generate_murhogrid.mGenerates voxel-based maps of optical and structural properties for Monte Carlo simulations. Geometry processing and voxelization READ_stl.mReads STL files and imports coral skeleton geometries into MATLAB. VOXELISE.mConverts surface-based coral geometries into a 3D voxel grid. get_surface_voxels.mIdentifies surface voxels defining the coral–water interface. splitCoralLayers.mSeparates coral skeleton structures into depth-resolved layers. Monte Carlo light transport modeling MC3D.mPrepares voxelized tissue models and input files for 3D Monte Carlo simulations. mcxyzn.cCore Monte Carlo photon transport engine that simulates light propagation through voxelized coral skeletons. mcxyzn.hHeader file defining structures and parameters used by the Monte Carlo engine. makemap.mGenerates custom colormaps for clear visualization of different material types and light fluence in 3D space. PAR_to_W_cm2.mConverts photon irradiance (PAR) into physical fluence units (W cm⁻²). Utility functions setgraph.mStandardizes plot formatting, axis labels, and figure appearance. cleanname.mSanitizes file and variable names for compatibility across scripts. OCT files calibration TIFF files.zip Contains OCT images of known reflectance standards and polystyrene microsphere suspensions. fungia_primary1.tiff-fungia_primary5.tiff OCT images of primary septa of the coral species Fungia fungites. fungia_secondary1.tiff-fungia_secondary5.tiff OCT images of primary septa of the coral species Fungia fungites. 3D coral fungia_fungites.stl 3D model of Fungia fungites derived from µCT scanning.