Realistic Modeling of Light Scattering in Brain Tissue and Ensuing Neuronal Excitation for Optogenetic Applications

Optogenetics has in recent years become a central tool in neuroscience research. Estimating the transmission of visible light through brain tissue is of crucial importance for designing and prediction the results of optogenetic experiments. The Kubelka-Munk model and Monte Carlo simulations have previously been used to model light propagation through rodents` brain tissue, however, these prior attempts suffer from fundamental shortcomings. Here, we introduce and study a new analytical approach for modeling the distributions of light emanating from a fiber and scattered through tissue. We demonstrate a good agreement of the new method`s predictions both with recently published data, and with new measurements in mouse brain cortical slices, that yield a new cortical scattering length estimate of ~47 µm at λ = 473 nm, significantly shorter than ordinarily assumed in optogenetic applications. Finally, we introduce a full neuronal simulation of optogenetic stimulation, which demonstrates that apical dendrites are responsible for the optogenetic excitation when illuminated from the cortex surface.