Authors: Zihao (John) Li and Christopher Fang-Yen
Affiliation: Department of Biomedical Engineering, The Ohio State University
Related publication: Li Z, Fang-Yen C. "Mechanisms of surface and volume light scattering from Caenorhabditis elegans revealed by angle-resolved measurements." iScience (2026). https://doi.org/10.1016/j.isci.2026.116117
Access this dataset on Dryad. DOI: 10.5061/dryad.s1rn8pkpj

Overview

This dataset contains raw experimental data, optical simulation results, 3D design files, and MATLAB analysis code from a study characterizing angle-resolved light scattering from C. elegans (a microscopic roundworm ~1 mm in length). Scattering measurements were taken across illumination angles θ = 0°–180° at three wavelengths (red 629 nm, green 516 nm, blue 447 nm) under varied substrate and index-matching conditions, allowing analysis of surface scattering (at the worm–environment interface) and volume scattering (within the worm body). Key quantities reported are the scattering function p(θ) and the contrast index. The scattering function has units of sr⁻¹ (inverse steradian) and describes the probability per unit solid angle of a photon being scattered by a polar angle θ relative to its original trajectory. The contrast index is dimensionless and quantifies how C. elegans appears different relative to its background in an image.

Contents in Worm-Scattering-main.zip

Dataset_S1/          Raw experimental and simulation data
Design_File_S1/      3D CAD files for modeling C. elegans and its surroundings
Software_S1/         Zemax OpticStudio simulation source files
Software_S2/         MATLAB data analysis scripts

Each subfolder contains a _README.txt with brief usage notes for the components in the folder.

Dataset S1

Common format: data.xlsx

All imaging measurement files are named data.xlsx and share the following columns: Position (cm, LED post reading used to compute illumination angle θ), Category ("worm" or "background"), Area (pixels, area of the region of interest), Mean (analog-to-digital units (ADU), mean pixel intensity of the region of interest), Min (ADU, minimum pixel intensity of the region of interest), Max (ADU, maximum pixel intensity of the region of interest), and Exposure (seconds, camera exposure time). Each row is the measurement for a worm or a background region.

Imaging data folders

Folders are named by imaging modality, substrate type, and whether index-matching was applied:

• BF (brightfield) — collects near-forward scattered light (θ = 0°).
• DF (darkfield) — collects off-axis forward scattered light (θ = 5°–65°).
• Backscat (backscatter) — collects light scattered back toward the light source (θ = 90°–180°).
• seeded — agar plates seeded with E. coli food bacteria; unseeded — agar plates without bacteria.
• idx_mat (index-matched) — worm surrounded by refractive-index-matched medium to suppress surface scattering; Non_idx_mat — standard conditions with both surface and volume scattering present.

Each folder contains data.xlsx files organized by color of illumination (red/, green/, blue/) and, where applicable, an index-matched subfolder. setting/ subfolders contain camera software screenshots for documentation of imaging parameter settings.

Power_Meter_data/

Power_Meter_data.xlsx — Incident optical power (µW) as a function of LED position, used to normalize scattering measurements. Three sheets (Red, Green, Blue), each with columns Position (cm), Reading (µW, raw power meter reading), N_LED_used (total number of LEDs activated during the experiment), and N_LED_measured (number of LEDs whose power was sampled by the power meter).

PIC/

PIC.mat — Camera calibration data containing the Pixel Irradiance Coefficient (PIC, units ADU·mm²·s⁻¹·µW⁻¹) for each illumination color (PIC_red, PIC_green, PIC_blue) and the power meter sensor area (Area_PM_sensor, mm²).

Zemax/

WSFC_zemax_N_10.mat — Results of 10 Zemax ray-tracing simulation runs of C. elegans scattering. Contains paired theta (degrees) and scattering function (sr⁻¹) arrays for three simulation conditions: index-matched/volume-only (theta_zemax_idxMat_N, WSFC_zemax_idxMat_N), surface-only (theta_zemax_ext_N, WSFC_zemax_ext_N), and full scattering (theta_zemax_full_N, WSFC_zemax_full_N).

Spatial_distribution/

MATLAB .mat files containing cross-sectional intensity profiles and the Edge-to-Mean Contrast Index as a function of illumination angle. EMCI > 0 indicates stronger scattering at body edges; EMCI < 0 indicates stronger scattering at body center.

Design File S1

STEP-format 3D CAD files for the object geometries used in Zemax optical simulation: Worm.step (worm body), Agar.step (agar substrate), Gel_pad_low.step and Gel_socket_low.step (components of index-matching gelatin media), WaterFilm_Low.step (water film around the worm). These files must be copied to the Zemax CAD files folder before running Software S1. Plain-text copies (.txt) of each file are provided for readability without CAD software.

Software S1

Ansys Zemax OpticStudio 2024 R2 simulation files. WormScat.zmx is the main project file defining the 3D optical system. WormScat_macro.ZPL is a ZPL macro that automates simulation runs across illumination angles; the output path must be set before running (instructions inside the file). Pre-computed simulation outputs are provided in Dataset_S1/Zemax/ and Dataset_S1/Spatial_distribution/. Plain-text copies (WormScat.txt and WormScat_macro.txt) are provided for readability without Zemax OpticStudio.

Setup: Copy .step files to Documents\Zemax\Objects\CAD Files and WormScat_macro.ZPL to Documents\Zemax\Macros.

Software S2

MATLAB scripts for data analysis and figure generation. Requires the Curve Fitting Toolbox and Statistics and Machine Learning Toolbox.

To reproduce figures: open Main.m, set main_work_dir and f_dataset_S1 to your local paths, then run each %% section.

Code/Software

The following software is required to open and run the files in this repository:

• Ansys Zemax OpticStudio 2024 R2 — required to open and run the simulation files in Software_S1/ and to view the 3D geometry files in Design_File_S1/.
• MATLAB R2025b — required to run the analysis scripts in Software_S2/ and to open .mat data files in Dataset_S1/. Requires the Curve Fitting Toolbox and Statistics and Machine Learning Toolbox.

Sharing/Access information

Links to other publicly accessible locations of the data: N/A

Data was derived from the following sources: N/A

This dataset is deposited on Dryad (https://doi.org/10.5061/dryad.s1rn8pkpj) in support of the manuscript:

Li Z, Fang-Yen C. "Mechanisms of surface and volume light scattering from Caenorhabditis elegans revealed by angle-resolved measurements." iScience (2026). https://doi.org/10.1016/j.isci.2026.116117