Deep Tissue Light Delivery and Fluorescence Tomography with Applications in Optogenetic Neurostimulation

Study of the brain microcircuits using optogenetics is an active area of research. This method has a few advantages over the conventional electrical stimulation including the bi-directional control of neural activity, and more importantly, specificity in neuromodulation. The first step in all optogenetic experiments is to express certain light sensitive ion channels/pumps in the target cell population and then confirm the proper expression of these proteins before running any experiment. Fluorescent bio-markers, such as green fluorescent protein (GFP), have been used for this purpose and co-expressed in the same cell population. The fluorescent signal from such proteins provides a monitory mechanism to evaluate the expression of optogenetic opsins over time. The conventional method to confirm the success in gene delivery is to sacrifice the animal, retract and slice the brain tissue, and image the corresponding slices using a fluorescent microscope. Obviously, determining the level of expression over time without sacrificing the animal is highly desirable. Also, optogenetics can be combined with cell-type specific optical recording of neural activity for example by imaging the fluorescent signal of genetically encoded calcium indicators. One challenging step in any optogenetic experiment is delivering adequate amount of light to target areas for proper stimulation of light sensitive proteins. Delivering sufficient light density to a target area while minimizing the off-target stimulation requires a precise estimation of the light distribution in the tissue. Having a good estimation of the tissue optical properties is necessary for predicting the distribution of light in any turbid medium. The first objective of this project was the design and development of a high resolution optoelectronic device to extract optical properties of rats\u27 brain tissue (including the absorption coefficient, scattering coefficient, and anisotropy factor) for three different wavelengths: 405nm, 532nm and 635nm and three different cuts: transverse, sagittal, and coronal. The database of the extracted optical properties was linked to a 3D Monte Carlo simulation software to predict the light distribution for different light source configurations. This database was then used in the next phase of the project and in the development of a fluorescent tomography scanner. Based on the importance of the fluorescent imaging in optogenetics, another objective of this project was to design a fluorescence tomography system to confirm the expression of the light sensitive proteins and optically recording neural activity using calcium indicators none or minimally invasively. The method of fluorescence laminar optical tomography (FLOT) has been used successfully in imaging superficial areas up to 2mm deep inside a scattering medium with the spatial resolution of ~200µm. In this project, we developed a FLOT system which was specifically customized for in-vivo brain imaging experiments. While FLOT offers a relatively simple and non-expensive design for imaging superficial areas in the brain, still it has imaging depth limited to 2mm and its resolution drops as the imaging depth increases. To address this shortcoming, we worked on a complementary system based on the digital optical phase conjugation (DOPC) method which was shown previously that is capable of performing fluorescent tomography up to 4mm deep inside a biological tissue with lateral resolution of ~50 µm. This system also provides a non-invasive method to deliver light deep inside the brain tissue for neurostimulation applications which are not feasible using conventional techniques because of the high level of scattering in most tissue samples. In the developed DOPC system, the performance of the system in focusing light through and inside scattering mediums was quantified. We also showed how misalignments and imperfections of the optical components can immensely reduce the capability of a DOPC setup. Then, a systematic calibration algorithm was proposed and experimentally applied to our DOPC system to compensate main aberrations such as reference beam aberrations and also the backplane curvature of the spatial light modulator. In a highly scattering sample, the calibration algorithm achieved up to 8 fold increase in the PBR

The Properties of Outer Retinal Band Three Investigated With Adaptive-Optics Optical Coherence Tomography.

PurposeOptical coherence tomography's (OCT) third outer retinal band has been attributed to the zone of interdigitation between RPE cells and cone outer segments. The purpose of this paper is to investigate the structure of this band with adaptive optics (AO)-OCT.MethodsUsing AO-OCT, images were obtained from two subjects. Axial structure was characterized by measuring band 3 thickness and separation between bands 2 and 3 in segmented cones. Lateral structure was characterized by correlation of band 3 with band 2 and comparison of their power spectra. Band thickness and separation were also measured in a clinical OCT image of one subject.ResultsBand 3 thickness ranged from 4.3 to 6.4 μm. Band 2 correlations ranged between 0.35 and 0.41 and power spectra of both bands confirmed peak frequencies that agree with histologic density measurements. In clinical images, band 3 thickness was between 14 and 19 μm. Measurements of AO-OCT of interband distance were lower than our corresponding clinical OCT measurements.ConclusionsBand 3 originates from a structure with axial extent similar to a single surface. Correlation with band 2 suggests an origin within the cone photoreceptor. These two observations indicate that band 3 corresponds predominantly to cone outer segment tips (COST). Conventional OCT may overestimate both the thickness of band 3 and outer segment length

Using Immune Genetic Algorithm in ATPG

Abstract: In this paper, an immune genetic based algorithm (IGA) for random test pattern generation was proposed. Genetic algorithms (GA) solve many search and optimization problems, effectively. However, they may drop into local optimal solutions; or they may find the optimal solution by low convergence speed. To overcome these problems, we used the immune concept and GA algorithm for random-based test generation. In the proposed algorithm, some of the main characteristics of the immune system were used to enhance the GA algorithm. As a result, a new random-based test pattern generation technique based on immune genetic algorithm (IGA) was presented. Experimental results showed that the proposed algorithm improved the ability of global search, avoided dropping into the local optimal solutions and increased the speed of computation convergence with respect to previously proposed non-immune GA algorithms. The proposed algorithm improved the test size with a factor of about 25 % in comparison with non-immune algorithms

Coextensive synchronized SLO-OCT with adaptive optics for human retinal imaging.

We describe the details of a multimodal retinal imaging system which combines adaptive optics (AO) with an integrated scanning light ophthalmoscopy (SLO) and optical coherence tomography (OCT) imaging system. The OCT subsystem consisted of a swept-source, Fourier-domain mode-locked (FDML) laser, with a very high A-scan rate (1.6 MHz), whose beam was raster scanned on the retina by two scanners-one resonant scanner and one galvanometer. The high sweep rate of the FDML permitted the SLO and OCT to utilize the same scanners for in vivo retinal imaging and, unlike existing multimodal systems, concurrently acquired SLO frames and OCT volumes with approximate en face correspondence at a rate of 6 Hz. The AO provided diffraction-limited cellular resolution for both imaging channels

Functional retinal imaging using adaptive optics swept-source OCT at 1.6 MHz.

Objective optical assessment of photoreceptor function may permit earlier diagnosis of retinal disease than current methods such as perimetry, electrophysiology, and clinical imaging. In this work, we describe an adaptive optics (AO) optical coherence tomography (OCT) system designed to measure functional responses of single cones to visible stimuli. The OCT subsystem consisted of a raster-scanning Fourier-domain mode-locked laser that acquires A scans at 1.64 MHz with a center wavelength of 1063 nm and an AO system operating in closed-loop. Analysis of serial volumetric images revealed phase changes of cone photoreceptors consistent with outer segment elongation and proportional to stimulus intensity, as well as other morphological changes in the outer segment and retinal pigment epithelium

Intraframe motion correction for raster-scanned adaptive optics images using strip-based cross-correlation lag biases.

In retinal raster imaging modalities, fixational eye movements manifest as image warp, where the relative positions of the beam and retina change during the acquisition of single frames. To remove warp artifacts, strip-based registration methods-in which fast-axis strips from target images are registered to a reference frame-have been applied in adaptive optics (AO) scanning light ophthalmoscopy (SLO) and optical coherence tomography (OCT). This approach has enabled object tracking and frame averaging, and methods have been described to automatically select reference frames with minimal motion. However, inconspicuous motion artifacts may persist in reference frames and propagate themselves throughout the processes of registration, tracking, and averaging. Here we test a previously proposed method for removing movement artifacts in reference frames, using biases in stripwise cross-correlation statistics. We applied the method to synthetic retinal images with simulated eye motion artifacts as well as real AO-SLO images of the cone mosaic and volumetric AO-OCT images, both affected by eye motion. In the case of synthetic images, the method was validated by direct comparison with motion-free versions of the images. In the case of real AO images, performance was validated by comparing the correlation of uncorrected images with that of corrected images, by quantifying the effect of motion artifacts on the image power spectra, and by qualitative examination of AO-OCT B-scans and en face projections. In all cases, the proposed method reduced motion artifacts and produced more faithful images of the retina