Mehdi Azimipour

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.

Closed-Loop Optogenetic Brain Interface

This paper presents a new approach for implementation of closed-loop brain-machine interface algorithms by combining optogenetic neural stimulation with electrocorticography and fluorescence microscopy. We used a new generation of microfabricated electrocorticography (micro-ECoG) devices in which electrode arrays are embedded within an optically transparent biocompatible substrate that provides optical access to the brain tissue during electrophysiology recording. An optical setup was designed capable of projecting arbitrary patterns of light for optogenetic stimulation and performing fluorescence microscopy through the implant. For realization of a closed-loop system using this platform, the feedback can be taken from electrophysiology data or fluorescence imaging. In the closed-loop systems discussed in this paper, the feedback signal was taken from the micro-ECoG. In these algorithms, the electrophysiology data are continuously transferred to a computer and compared with some predefined spatial-temporal patterns of neural activity. The computer which processes the data also readjusts the duration and distribution of optogenetic stimulating pulses to minimize the difference between the recorded activity and the predefined set points so that after a limited period of transient response the recorded activity follows the set points. Details of the system design and implementation of typical closed-loop paradigms are discussed in this paper.

OptogenSIM: a 3D Monte Carlo simulation platform for light delivery design in optogenetics.

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.

Patterned optogenetic modulation of neurovascular and metabolic signals

The hemodynamic and metabolic response of the cortex depends spatially and temporally on the activity of multiple cell types. Optogenetics enables specific cell types to be modulated with high temporal precision and is therefore an emerging method for studying neurovascular and neurometabolic coupling. Going beyond temporal investigations, we developed a microprojection system to apply spatial photostimulus patterns in vivo. We monitored vascular and metabolic fluorescence signals after photostimulation in Thy1-channelrhodopsin-2 mice. Cerebral arteries increased in diameter rapidly after photostimulation, while nearby veins showed a slower smaller response. The amplitude of the arterial response was depended on the area of cortex stimulated. The fluorescence signal emitted at 450/100 nm and excited with ultraviolet is indicative of reduced nicotinamide adenine dinucleotide, an endogenous fluorescent enzyme involved in glycolysis and the citric acid cycle. This fluorescence signal decreased quickly and transiently after optogenetic stimulation, suggesting that glucose metabolism is tightly locked to optogenetic stimulation. To verify optogenetic stimulation of the cortex, we used a transparent substrate microelectrode array to map cortical potentials resulting from optogenetic stimulation. Spatial optogenetic stimulation is a new tool for studying neurovascular and neurometabolic coupling.

Calibration of digital optical phase conjugation setups based on orthonormal rectangular polynomials

Digital optical phase conjugation (DOPC) has proven to be a promising technique in deep tissue fluorescence imaging. Nonetheless, DOPC optical setups require precise alignment of all optical components to accurately read the wavefront of scattered light in a turbid medium and playback the conjugated beam toward the sample. Minor misalignments and possible imperfections in the arrangement or the structure of the optical components significantly reduce the performance of the method. In this paper, a calibration procedure based on orthogonal rectangular polynomials is introduced to compensate major imperfections including the optical aberration in the wavefront of the reference beam and the substrate curvature of the spatial light modulator without adding extra optical components to the original setup. The proposed algorithm also provides a systematic calibration procedure for mechanical fine tuning of DOPC systems. It is shown experimentally that the proposed calibration process improves the peak-to-background ratio when focusing light after passing through a highly scattering medium.

Effect of blood vessels on light distribution in optogenetic stimulation of cortex.

In this Letter, the impact of blood vessels on light distribution during photostimulation of cortical tissue in small rodents is investigated. Brain optical properties were extracted using a double-integrating sphere setup, and optical coherence tomography was used to image cortical vessels and capillaries to generate a three-dimensional angiogram of the cortex. By combining these two datasets, a complete volumetric structure of the cortical tissue was developed and linked to a Monte Carlo code which simulates light propagation in this inhomogeneous structure and illustrates the effect of blood vessels on the penetration depth and pattern preservation in optogenetic stimulation.

Fluorescence laminar optical tomography for brain imaging: system implementation and performance evaluation

Abstract. 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.

Nonlinear optical signal processing on multiwavelength sensitive materials.

Exploiting salient features in the photodynamics of specific types of light sensitive materials, a new approach is presented for realization of parallel nonlinear operations with optics. We briefly review the quantum structure and mathematical models offered for the photodynamics of two multiwavelength sensitive materials, doped crystals of lithium niobate and thick layers of bacteriorhodopsin. Next, a special mode of these dynamics in each material is investigated and a graphical design procedure is offered to produce highly nonlinear optical responses that can be dynamically reshaped via applying minimum changes in the optical setup.

Light pattern preservation in rodent's cortical tissue during optogenetic neuro-stimulation(Conference Presentation)

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.

Monitoring hemodynamic changes in stroke-affected muscles using near-infrared spectroscopy

The oxygenation level of a tissue is an important marker of the health of the tissue and has a direct effect on performance. It has been shown that the blood flow to the paretic muscles of hemiparetic post-stroke patients is significantly reduced compared to non-paretic muscles. It is hypothesized that hemodynamic activity in paretic muscles is suppressed as compared to non-paretic muscles, and that oximetry can be used to measure this disparity in real-time. In order to test this hypothesis, a custom-made oximetry device was used to measure hemodynamic activity in the forearm extensor muscles in post-stroke patients’ paretic and non-paretic sides and in a control population during three exercise levels calibrated to the subject’s maximum effort. The change in oxygenation (ΔOxy) and blood volume (ΔBV) were calculated and displayed in real-time. Results show no apparent difference in either ΔOxy or ΔBV between control subjects’ dominant and non-dominant muscles. However, the results show a significant difference in ΔOxy between paretic and non-paretic muscles, as well as a significant difference between normalized post-stroke and control data. Further work will be necessary to determine if the observed difference between the paretic and non-paretic muscles changes over the course of physical therapy and can be correlated with functional improvements.