Implantable Neural Probes for Electrical Recording and Optical Stimulation of Cellular Level Neural Circuitry in Behaving Animals.

In order to advance the understanding of brain function, it is critical to monitor how neural circuits work together and perform computational processing. For the past few decades, a wide variety of neural probes have been developed to study the electrophysiology of the brain. This work is focused on two important objectives to improve the brain-computer interface: 1) to enhance the reliability of recording electrodes by optimizing the shank structure; 2) to incorporate optical stimulation capability in addition to electrical recording for applications involving optogenetics. For the first objective, a flexible 64-channel parylene probe was designed with unique geometries for reduced tissue reactions. In order to provide the mechanical stiffness necessary to penetrate the brain, the miniaturized, flexible probes were coated with a lithographically patterned silk fibroin, which served as a biodegradable insertion shuttle. Because the penetration strength is independent from the properties of the probe itself, the material and geometry of the probe structure can be optimally designed without constraints. These probes were successfully implanted into the layer-V of motor cortex in 6 rats and recorded neural activities in vivo for 6 weeks. For the second objective, either optical waveguides or μLEDs were monolithically integrated on the probe shanks for optogenetic applications. Compared to existing methods, this work can offer high spatial-temporal resolution to record and stimulate from even subcellular neural structures. In the experiments using wild type animals, despite optimized recording of spontaneous neural activities, the cells never responded to illumination. In contrast, for the ChR2 expressed animals, light activation of neural activities was extremely robust and local, which phase-locked to the light waveform whenever the cell was close to the light source. In particular, the probes integrated with μLEDs were capable of driving different neural circuit behaviors using two adjacent μLEDs separated only by a 60-μm-pitch. With 3 μLEDs integrated at the tip of each of the 4 probe shanks, this novel optogenetic probe can provide more than 480 million (12!) different spiking sequences at the sub-cellular resolution, which is ideal to manipulate high density neural network with versatility and precision.PhDElectrical EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/111604/1/wufan_1.pd

Depth-specific optogenetic control in vivo with a scalable, high density µLED neural probe

Controlling neural circuits is a powerful approach to uncover a causal link between neural activity and behaviour. Optogenetics has been widely adopted by the neuroscience community as it offers cell-type-specific perturbation with millisecond precision. However, these studies require light delivery in complex patterns with cellular-scale resolution, while covering a large volume of tissue at depth in vivo. Here we describe a novel high-density silicon-based microscale light-emitting diode (µLED) array, consisting of up to ninety-six 25 µm-diameter µLEDs emitting at a wavelength of 450 nm with a peak irradiance of 400 mW/mm2. A width of 100 µm, tapering to a 1 µm point, and a 40 µm thickness help minimise tissue damage during insertion. Thermal properties permit a set of optogenetic operating regimes, with ~0.5°C average temperature increase. We demonstrate depth-dependent activation of mouse neocortical neurons in vivo, offering an inexpensive novel tool for the precise manipulation of neural activity

Technological challenges in the development of optogenetic closed-loop therapy approaches in epilepsy and related network disorders of the brain

Epilepsy is a chronic, neurological disorder affecting millions of people every year. The current available pharmacological and surgical treatments are lacking in overall efficacy and cause side-effects like cognitive impairment, depression, tremor, abnormal liver and kidney function. In recent years, the application of optogenetic implants have shown promise to target aberrant neuronal circuits in epilepsy with the advantage of both high spatial and temporal resolution and high cell-specificity, a feature that could tackle both the efficacy and side-effect problems in epilepsy treatment. Optrodes consist of electrodes to record local field potentials and an optical component to modulate neurons via activation of opsin expressed by these neurons. The goal of optogenetics in epilepsy is to interrupt seizure activity in its earliest state, providing a so-called closed-loop therapeutic intervention. The chronic implantation in vivo poses specific demands for the engineering of therapeutic optrodes. Enzymatic degradation and glial encapsulation of implants may compromise long-term recording and sufficient illumination of the opsin-expressing neural tissue. Engineering efforts for optimal optrode design have to be directed towards limitation of the foreign body reaction by reducing the implant’s elastic modulus and overall size, while still providing stable long-term recording and large-area illumination, and guaranteeing successful intracerebral implantation. This paper presents an overview of the challenges and recent advances in the field of electrode design, neural-tissue illumination, and neural-probe implantation, with the goal of identifying a suitable candidate to be incorporated in a therapeutic approach for long-term treatment of epilepsy patients

Optoelectronic Neural Implant Sensors for Cerebral Blood Volume Monitoring

Nearly 50 million people are afflicted with epilepsy, worldwide. These patients suffer from unprovoked seizures, where neurons in the cerebral cortex under go uncontrolled, hypersynchronous firing of neurons. 30\% of patients with epilepsy do not respond to drug treatments. For these patients, surgical treatment involving the removal or disconnection of brain matter is one of the only alternatives. Such surgical treatments often rely on long-term monitoring of neuronal activity in the brain using subdurally implanted surface electrodes to locate the epileptic focus, but these clinical methods for mapping neuronal activity suffer from low spatial resolutions and poor noise, which can limit the success of surgical treatments where an error of even 1 mm can be critical. The work described here involves the development of an implantable system for performing optical recordings of intrinsic signal (ORIS) on the surface of the brain. By taking advantage of the unique absorption spectrum of hemoglobin, cerebral blood volume (CBV) can be measured via reflectivity changes in the brain at at specific wavelengths of light. Due to the metabolic demands of the brain, the exaggerated neuronal activity and spiking associated with epileptic seizures can be detected indirectly through changes in CBV. While high resolution ORIS measurements have been recorded using externally mounted CCD sensors, this work presents some of the first developments in producing a fully implantable ORIS sensor. Progress in the development of an implantable ORIS sensor described here includes: an implantable organic light emitting diode (OLED) and organic photodetector (OPD) integrated on a highly flexible parylene-c substrate, an implantable sensor using a microLED array embedded on a flexible polyimide substrate, and the application of quantum dots to microLEDs for optical down-conversion. Successful in vivo detection of seizures is achieved with high signal-to-noise using these methods. Additionally, spatial localization of seizure activity is performed using the microLED array. These developments represent crucial first steps in the development of a full 2D neuronal mapping system using implantable ORIS devices

Biointegrated and wirelessly powered implantable brain devices: a review

Implantable neural interfacing devices have added significantly to neural engineering by introducing the low-frequency oscillations of small populations of neurons known as local field potential as well as high-frequency action potentials of individual neurons. Regardless of the astounding progression as of late, conventional neural modulating system is still incapable to achieve the desired chronic in vivo implantation. The real constraint emerges from mechanical and physical diffierences between implants and brain tissue that initiates an inflammatory reaction and glial scar formation that reduces the recording and stimulation quality. Furthermore, traditional strategies consisting of rigid and tethered neural devices cause substantial tissue damage and impede the natural behaviour of an animal, thus hindering chronic in vivo measurements. Therefore, enabling fully implantable neural devices, requires biocompatibility, wireless power/data capability, biointegration using thin and flexible electronics, and chronic recording properties. This paper reviews biocompatibility and design approaches for developing biointegrated and wirelessly powered implantable neural devices in animals aimed at long-term neural interfacing and outlines current challenges toward developing the next generation of implantable neural devices

Implantable Low-Noise Fiberless Optoelectrodes for Optogenetic Control of Distinct Neural Populations

The mammalian brain is often compared to an electrical circuit, and its dynamics and function are governed by communication across different types neurons. To treat neurological disorders like Alzheimer’s and Parkinson’s, which are characterized by inhibition or amplification of neural activity in a particular region or lack of communication between different regions of the brain, there is a need to understand troubleshoot neural networks at cellular or local circuit level. In this work, we introduce a novel implantable optoelectrode that can manipulate more than one neuron type at a single site, independently and simultaneously. By delivering multi-color light using a scalable optical waveguide mixer, we demonstrate manipulation of multiple neuron types at precise spatial locations in vivo for the first time. We report design, micro-fabrication and optoelectronic packaging of a fiber-less, multicolor optoelectrode. The compact optoelectrode design consists of a 7 μm x 30 μm dielectric optical waveguide mixer and eight electrical recording sites monolithically integrated on each shank of a 22 μm-thick four-shank silicon neural probe. The waveguide mixers are coupled to eight side-emitting injection laser diodes (ILDs) via gradient-index (GRIN) lenses assembled on the probe backend. GRIN-based optoelectrode enables efficient optical coupling with large alignment tolerance to provide wide optical power range (10 to 3000 mW/mm2 irradiance) at stimulation ports. It also keeps thermal dissipation and electromagnetic interference generated by light sources sufficiently far from the sensitive neural signals, allowing thermal and electrical noise management on a multilayer printed circuit board. We demonstrated device verification and validation in CA1 pyramidal layer of mice hippocampus in both anesthetized and awake animals. The packaged devices were used to manipulate variety of multi-opsin preparations in vivo expressing different combinations of Channelrhodopsin-2, Archaerhodopsin and ChrimsonR in pyramidal and parvalbumin interneuron cells. We show effective stimulation, inhibition and recording of neural spikes at precise spatial locations with less than 100 μV stimulation-locked transients on the recording channels, demonstrating novel use of this technology in the functional dissection of neural circuits.PHDBiomedical EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/137171/1/kkomal_1.pd

Three-dimensional, multifunctional neural interfaces for cortical spheroids and engineered assembloids.

Three-dimensional (3D), submillimeter-scale constructs of neural cells, known as cortical spheroids, are of rapidly growing importance in biological research because these systems reproduce complex features of the brain in vitro. Despite their great potential for studies of neurodevelopment and neurological disease modeling, 3D living objects cannot be studied easily using conventional approaches to neuromodulation, sensing, and manipulation. Here, we introduce classes of microfabricated 3D frameworks as compliant, multifunctional neural interfaces to spheroids and to assembloids. Electrical, optical, chemical, and thermal interfaces to cortical spheroids demonstrate some of the capabilities. Complex architectures and high-resolution features highlight the design versatility. Detailed studies of the spreading of coordinated bursting events across the surface of an isolated cortical spheroid and of the cascade of processes associated with formation and regrowth of bridging tissues across a pair of such spheroids represent two of the many opportunities in basic neuroscience research enabled by these platforms

Evaluation of ultrasound sensors for transcranial photoacoustic sensing and imaging

Biomedical photoacoustic (PA) imaging is typically used to exploit absorption-based contrast in soft tissue at depths of several centimeters. When it is applied to measuring PA waves generated in the brain, the acoustic properties of the skull bone cause not only strong attenuation but also a distortion of the wavefront, which diminishes image resolution and contrast. This effect is directly proportional to bone thickness. As a result, transcranial PA imaging in humans has been challenging to demonstrate. We measured the acoustic constraints imposed by the human skull to design an ultrasound sensor suitable for transcranial PA imaging and sensing. We imaged the phantoms using a planar Fabry-Perot sensor and employed a range of piezoelectric and optical ultrasound sensors to measure the frequency dependent acoustic transmission through human cranial bone. Transcranial PA images show typical frequency and thickness dependent attenuation and aberration effects associated with acoustic propagation through bone. The skull insertion loss measurements showed significant transmission at low frequencies. In comparison to conventional piezoelectric sensors, the performance of plano-concave optical resonator (PCOR) ultrasound sensors was found to be highly suitable for transcranial PA measurements. They possess high acoustic sensitivity at a low acoustic frequency range that coincides with the transmission window of human skull bone. PCOR sensors showed low noise equivalent pressures and flat frequency response which enabled them to outperform conventional piezoelectric transducers in transcranial PA sensing experiments. Transcranial PA sensing and imaging requires ultrasound sensors with high sensitivity at low acoustic frequencies, and a broad and ideally uniform frequency response. We designed and fabricated PCOR sensors and demonstrated their suitability for transcranial PA sensing

Novel Tools to Investigate Cortical Activity in Paroxysmal Disorders

This PhD project is at the interface between academic research and industry, and is jointly sponsored by the BBSRC and the industrial partner– Scientifica UK. The goal of this research is the development of new instruments and approaches to monitor and manipulate neuronal network activity in disease states. Firstly, (I) I collaborated with Scientifica to develop and utilise the newly developed Laser Applied Stimulation and Uncaging (LASU) system. The combined usage of the LASU system, alongside novel spatially-targeted channelrhodopsin variants, has al- lowed me to test the limits of single-photon optogenetic stimulation in achieving specific activation of targeted neurons. The presented findings demonstrate that, al- though high-resolution stimulation is achievable in the rodent cortex, single-photon stimulation is insufficient to achieve single-cell resolution stimulation. Secondly, (II) I have combined the high temporal resolution of novel, transparent 16-channel epicortical graphene solution-gated field effect transistor (gSGFET) arrays with the large spatial coverage of bilateral widefield Ca2+ fluorescence imaging; to per- form investigations of the relationship between spreading depolarisation (SD) and cortical seizures in awake head-fixed mouse models of epilepsy. To analyse these complex datasets, I developed a bespoke, semi-automated analysis pipeline to pro- cess the data and probe the seizure-SD relationship. I present the advantages of this dual-modality approach by demonstrating the strengths and weaknesses of each recording method, and how a synergistic approach overcomes the limitations of each technique alone. I utilise widefield imaging to perform systematic classification of SD and seizures both temporally and spatially. Detailed electrophysiological anal- ysis of gSGFET data is then performed on extracted time periods of interest. This work demonstrates the complex interaction between seizures and SD, and proposes several mechanisms describing these interactions. The technological and analytical tools presented here lay the groundwork for insightful and flexible experimental paradigms; altogether, able to probe paroxysmal activity in profound detail

The visible and near-infrared optical absorption coefficient spectrum of Parylene C measured by transmitting light through thin films in liquid filled cuvettes

Parylene C (PPXC) is a polymer deposited from the gas phase to form optically clear thin films used in devices including waveguides and sensors. The performance of these devices depends on the visible and near infrared absorption coefficient of PPXC. However, the absorption coefficient is difficult to measure. This is because PPXC films are typically too thin to exhibit detectable absorption in conventional transmittance measurements. To address this challenge, a method involving measuring the transmittance of multiple films immersed together in a liquid filled cuvette was devised. This increased the sensitivity to absorption by increasing the path length in PPXC, while also minimizing reflections and surface losses. Using 200-500 µm thick films, this method was applied to measure the absorption coefficient of PPXC at wavelengths in the range 330-3300 nm. The coefficient was found to vary spectrally by more than two orders of magnitude from 0.025 mm-1 at 1562 nm to 7.7 mm-1 at 3262 nm. These absorption measurements could aid the design of PPXC based sensors and waveguides. The method could be useful for measuring the absorption coefficient of other thin, low-loss materials, particularly those for which it is challenging to obtain thick samples such as other polymers deposited from the gas phase in a similar manner to PPXC