Research Article

Simulating 3D refractive index distributions of suspended cells

CNR-ISASI, Institute of Applied Sciences and Intelligent Systems “Eduardo Caianiello”, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy

^* Corresponding authors: This email address is being protected from spambots. You need JavaScript enabled to view it. (Francesca Borrelli); This email address is being protected from spambots. You need JavaScript enabled to view it. (Pietro Ferraro)

Received: 23 July 2025
Accepted: 26 September 2025

Abstract

The introduction of holo-tomographic flow cytometry has unlocked the possibility of imaging the 3D refractive index (RI) distribution of suspended cells while they flow and rotate in microfluidic streams. Similarly, approaches that optically trap and rotate the samples can image them in suspension conditions. Great effort has been spent in developing robust algorithms for the tomogram estimation, as well as denoising and 3D segmentation algorithms. However, the lack of a ground-truth dataset for suspended cells significantly hinders the development of image processing pipelines, limiting the advancement of the associated technology field. Here we propose a novel method for simulating 3D refractive index distribution of suspended cells. We start with prior knowledge of the statistics of the 3D RI profile and morphometry of various cell sub-compartments gathered from holo-tomographic flow cytometry experiments and combined with literature data to create their 3D distributions. As a benchmark for the simulator, we created a shared dataset of RI cell models with various levels of complexity, simulating yeast eukaryotic cells at different budding stages with various phenotypes of cytoplasmic vacuoles, and the presence of cytoplasmic vacuoles, lipid droplets and lysosomes in monocyte cells.