A Computational Model of Light-Sheet Fluorescence Microscopy using Physically-based Rendering

Abstract

We present a physically-based computational model of the light sheet fluorescence microscope (LSFM). Based on Monte Carlo ray tracing and geometric optics, our method simulates the operational aspects and image formation process of the LSFM. An extension for previous fluorescence models is developed to account for the intrinsic characteristics of fluorescent dyes in order to accurately simulate light interaction with fluorescent-tagged biological specimen. This extension was quantitatively validated against the fluorescence brightness equation and experimental spectra of different dyes. We demonstrate first results of our rendering pipeline to a simplified brain tissue model reconstructed from the somatosensory cortex of a young rat.