title: Extraction of optical properties and prediction of light distribution in rat brain tissue.
abstract: Predicting the distribution of light inside any turbid media, such as biological tissue, requires detailed information about the optical properties of the medium, including the absorption and scattering coefficients and the anisotropy factor. Particularly, in biophotonic applications where photons directly interact with the tissue, this information translates to system design optimization, precision in light delivery, and minimization of unintended consequences, such as phototoxicity or photobleaching. In recent years, optogenetics has opened up a new area in deep brain stimulation with light and the method is widely adapted by researchers for the study of the brain circuitries and the dynamics of neurological disorders. A key factor for a successful optogenetic stimulation is delivering an adequate amount of light to the targeted brain objects. The adequate amount of light needed to stimulate each brain object is identified by the tissue optical properties as well as the type of opsin expressed in the tissue, wavelength of the light, and the physical dimensions of the targeted area. Therefore, to implement a precise light delivery system for optogenetics, detailed information about the optical properties of the brain tissue and a mathematical model that incorporates all determining factors is needed to find a good estimation of light distribution in the brain. In general, three measurements are required to obtain the optical properties of any tissue, namely diffuse transmitted light, diffuse reflected light, and transmitted ballistic beam. In this report, these parameters were measured in vitro using intact rat brain slices of 500 μm thickness via a two-integrating spheres optical setup. Then, an inverse adding doubling method was used to extract the optical properties of the tissue from the collected data. These experiments were repeated to cover the whole brain tissue with high spatial resolution for the three different cuts (transverse, sagittal, and coronal) and three different wavelengths (405, 532, and 635 nm) in the visible range of the spectrum. A three-dimensional atlas of the rat brain optical properties was constructed based on the experimental measurements. This database was linked to a Monte Carlo toolbox to simulate light distribution in the tissue for different light source configurations.
authors.affiliation: University of Wisconsin-Milwaukee, Electrical and Computer Engineering Department, Milwaukee, Wisconsin 53211.
authors.forename: Mehdi
authors.initials: M
authors.lastname: Azimipour
authors.affiliation: University of Wisconsin-Milwaukee, Electrical and Computer Engineering Department, Milwaukee, Wisconsin 53211.
authors.forename: Ryan
authors.initials: R
authors.lastname: Baumgartner
authors.affiliation: University of Wisconsin at Madison, Laboratory for Optical and Computational Instrumentation, 1675 Observatory Drive, Madison, Wisconsin 53706.
authors.forename: Yuming
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Oregon Health Science University, Department of Biomedical Engineering, 3303 SW Bond Avenue, Portland, Oregon 97239dOregon Health Science University, Department of Dermatology, 3303 SW Bond Avenue, Portland, Oregon 97239.
authors.forename: Steven L
authors.initials: SL
authors.lastname: Jacques
authors.affiliation: University of Wisconsin at Madison, Laboratory for Optical and Computational Instrumentation, 1675 Observatory Drive, Madison, Wisconsin 53706.
authors.forename: Kevin
authors.initials: K
authors.lastname: Eliceiri
authors.affiliation: University of Wisconsin-Milwaukee, Electrical and Computer Engineering Department, Milwaukee, Wisconsin 53211.
authors.forename: Ramin
authors.initials: R
authors.lastname: Pashaie
mesh_terms: D000818:Animals; D016880:Anisotropy; D001921:Brain / Q000502:physiology*; D003198:Computer Simulation; D016208:Databases, Factual; D005260:Female; D007091:Image Processing, Computer-Assisted; D008027:Light; D009010:Monte Carlo Method; D061848:Optical Imaging / Q000379:methods*; D019047:Phantoms, Imaging; D051381:Rats; D017207:Rats, Sprague-Dawley; D012542:Scattering, Radiation