title: OptogenSIM: a 3D Monte Carlo simulation platform for light delivery design in optogenetics.
abstract: Optimizing light delivery for optogenetics is critical in order to accurately stimulate the neurons of interest while reducing nonspecific effects such as tissue heating or photodamage. Light distribution is typically predicted using the assumption of tissue homogeneity, which oversimplifies light transport in heterogeneous brain. Here, we present an open-source 3D simulation platform, OptogenSIM, which eliminates this assumption. This platform integrates a voxel-based 3D Monte Carlo model, generic optical property models of brain tissues, and a well-defined 3D mouse brain tissue atlas. The application of this platform in brain data models demonstrates that brain heterogeneity has moderate to significant impact depending on application conditions. Estimated light density contours can show the region of any specified power density in the 3D brain space and thus can help optimize the light delivery settings, such as the optical fiber position, fiber diameter, fiber numerical aperture, light wavelength and power. OptogenSIM is freely available and can be easily adapted to incorporate additional brain atlases.
authors.affiliation: Laboratory for Optical and Computational Instrumentation, Department of Biomedical Engineering, University of Wisconsin at Madison, 1675 Observatory Drive, Madison, WI 53706, USA.
authors.forename: Yuming
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Biomedical Engineering, Oregon Health and Science University, 3303 SW Bond Ave, Portland, OR 97239, USA ; Department of Dermatology, Oregon Health and Science University, 3303 SW Bond Ave, Portland, OR 97239, USA.
authors.forename: Steven L
authors.initials: SL
authors.lastname: Jacques
authors.affiliation: Electrical Engineering Department, University of Wisconsin-Milwaukee, 3200 N Cramer St., Milwaukee, Wisconsin 53211, USA.
authors.forename: Mehdi
authors.initials: M
authors.lastname: Azimipour
authors.affiliation: Laboratory for Optical and Computational Instrumentation, Department of Biomedical Engineering, University of Wisconsin at Madison, 1675 Observatory Drive, Madison, WI 53706, USA.
authors.forename: Jeremy D
authors.initials: JD
authors.lastname: Rogers
authors.affiliation: Electrical Engineering Department, University of Wisconsin-Milwaukee, 3200 N Cramer St., Milwaukee, Wisconsin 53211, USA.
authors.forename: Ramin
authors.initials: R
authors.lastname: Pashaie
authors.affiliation: Laboratory for Optical and Computational Instrumentation, Department of Biomedical Engineering, University of Wisconsin at Madison, 1675 Observatory Drive, Madison, WI 53706, USA ; Morgridge Institute for Research, 330 North Orchard Street, Madison, WI 53715, USA.
authors.forename: Kevin W
authors.initials: KW
authors.lastname: Eliceiri
keywords: (080.1753) Computation methods; (170.2945) Illumination design; (170.3660) Light propagation in tissues; (170.4090) Modulation techniques