We present our effort in implementing a fluorescence laminar optical tomography scanner which is specifically designed for noninvasive three-dimensional imaging of fluorescence proteins in the brains of small rodents. A laser beam, after passing through a cylindrical lens, scans the brain tissue from the surface while the emission signal is captured by the epi-fluorescence optics and is recorded using an electron multiplication CCD sensor. Image reconstruction algorithms are developed based on Monte Carlo simulation to model light–tissue interaction and generate the sensitivity matrices. To solve the inverse problem, we used the iterative simultaneous algebraic reconstruction technique. The performance of the developed system was evaluated by imaging microfabricated silicon microchannels embedded inside a substrate with optical properties close to the brain as a tissue phantom and ultimately by scanning brain tissue in vivo. Details of the hardware design and reconstruction algorithms are discussed and several experimental results are presented. The developed system can specifically facilitate neuroscience experiments where fluorescence imaging and molecular genetic methods are used to study the dynamics of the brain circuitries.
Optogenetics provides a tool for modulating activity of specific cell types by light pulses. Different light delivery mechanisms such as single optical fiber implanted on a skull or patterned illumination can be employed to direct light to a target area. For a highly scattering medium such as brain tissue, light distribution significantly depends on the scattering parameters of the tissue as well as the inherent inhomogeneity of the specimen. For in vivo studies, blood vessels which have considerable absorption coefficient in the visible spectrum play a major role in producing such inhomogeneity. Therefore, detailed information about brain optical properties and network of blood vessels which was ignored in previous studies is necessary to accurately predict light distribution and designing light delivery mechanism during optogenetic experiments to achieve the desired optical stimulation. In this paper, light pattern preservation while considering the impact of blood vessels is investigated in a rat cortex. First, the typical optical properties of rat cortical tissue were extracted by employing double integrated sphere technique, and then, optical coherence tomography was employed to obtain structure of blood vessels on the cortex. By combining the extracted optical properties and the network of blood vessels, a three-dimensional model of a rat cortical tissue was developed. Then, a Monte Carlo simulation code was used to predict light distribution in this model for different light source configurations and wavelengths. The results confirm that presence of vessels can significantly impact the light pattern in the tissue and affect the practical depth of penetration.
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.
In this article we present a new approach for implementation of computation algorithms to perform nonlinear signal processing with light on the surface of a photorefractive crystal and Bacteriorhodopsin thin film. Using the developed mathematical models for the photodynamics of these materials, we demonstrate a specific operation mode and a design procedure to obtain nonlinear response which can be used for implementation of high-performance photonic computers.