Field measurements of scattering and absorptive biological samples

This dataset contains field measurements, captured with angular diversity, of scattering and absorptive biological samples. It is supplemental data to the publication linked below which demonstrates reconstructions of complex-valued refractive index mappings in a variety of biological samples. Included in this dataset are angular diversity field measurements of: Micrasterias Radiata - Unicellular algae. Dominant absorber is chlorophyll. Succulent - Common succulent plant sectioned under a vibratome. Dominant absorber is chlorophyll. Zebrafish Embryo 48 hpf - Fixed Zebrafish Embryo 48 hpf. Dominant absorber is melanin. To reproduce the results from the main text, please follow the steps below: 1. Download the code from the GitHub repository (https://github.com/ut-cwo/Inverse-scattering-of-absorptive-samples-via-beam-propagation). Parameter files for each sample can be found alongside the code. 2. Download a dataset below. Due to the size of these files, they can only be downloaded one at a time. 3. Follow the instructions in mainMSBP.m for pathing and reconstruction. For use outside of this codebase, the format of the data is provided below; it is stored as a '.mat' (-v7.3) variable file with the following structure: Efield_amplitude - 3D numeric array holding a background subtracted 2D amplitude measurement for each angle. [Y, X, Angles] (float) Efield_phase - 3D numeric array holding a background subtracted 2D phase measurement for each angle. This demodulates the field to DC. [Y, X, Angles] (float) fx_illum_ref - fx components of illumination angles. [1, Angles] (float) fy_illum_ref - fy components of illumination angles. [1, Angles] (float) ps - Pixel size in [um] (float) lambda - Wavelength in [um] (float) NA - Numerical aperture (float) n_m - Refractive index of sample media (float) n_imm - Refractive index of immersion (float) Loading '.mat' (-v7.3) variable files outside of MATLAB can be easily accomplished using external libraries. For example, the Python library, mat73, reads the stored variables as key-value pairs. If this dataset is useful to you, please consider citing: Wagenaar, Peter, et al. "Inverse-scattering of absorptive samples via beam propagation." bioRxiv (2026). Acknowledgements: Thanks to Jeongsu Kim for providing these measurements.