Configuring the light power emitted from the optical fiber is an essential first step in planning in-vivo optogenetic
experiments. However, diffusion theory, which was adopted for optogenetic research, precluded accurate estimates of
light intensity in the semi-diffusive region where the primary locus of the stimulation is located. We present a 3D Monte
Carlo model that provides an accurate and direct solution for light distribution in this region. Our method directly records
the photon trajectory in the separate volumetric grid planes for the near-source recording efficiency gain, and it
incorporates a 3D brain mesh to support both homogeneous and heterogeneous brain tissue. We investigated the light
emitted from optical fibers in brain tissue in 3D, and we applied the results to design optimal light delivery parameters
for precise optogenetic manipulation by considering the fiber output power, wavelength, fiber-to-target distance, and the
area of neural tissue activation.
Younghoon Shin, Dongmok Kim, Jihoon Lee, and Hyuk-Sang Kwon, "3D Monte Carlo model with direct photon flux recording for optimal optogenetic light delivery," Proc. SPIE 10052, Optogenetics and Optical Manipulation, 100520G (Presented at SPIE BiOS: January 29, 2017; Published: 8 February 2017); https://doi.org/10.1117/12.2250679.
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