Photonic neural probe enabled microendoscopes for light-sheet light-field computational fluorescence brain imaging

Significance

Light-sheet fluorescence microscopy is widely used for high-speed, high-contrast, volumetric imaging. Application of this technique to in vivo brain imaging in non-transparent organisms has been limited by the geometric constraints of conventional light-sheet microscopes, which require orthogonal fluorescence excitation and collection objectives. We have recently demonstrated implantable photonic neural probes that emit addressable light sheets at depth in brain tissue, miniaturizing the excitation optics. Here, we propose a microendoscope consisting of a light-sheet neural probe packaged together with miniaturized fluorescence collection optics based on an image fiber bundle for lensless, light-field, computational fluorescence imaging.

Aim

Foundry-fabricated, silicon-based, light-sheet neural probes can be packaged together with commercially available image fiber bundles to form microendoscopes for light-sheet light-field fluorescence imaging at depth in brain tissue.

Approach

Prototype microendoscopes were developed using light-sheet neural probes with five addressable sheets and image fiber bundles. Fluorescence imaging with the microendoscopes was tested with fluorescent beads suspended in agarose and fixed mouse brain tissue.

Results

Volumetric light-sheet light-field fluorescence imaging was demonstrated using the microendoscopes. Increased imaging depth and enhanced reconstruction accuracy were observed relative to epi-illumination light-field imaging using only a fiber bundle.

Conclusions

Our work offers a solution toward volumetric fluorescence imaging of brain tissue with a compact size and high contrast. The proof-of-concept demonstrations herein illustrate the operating principles and methods of the imaging approach, providing a foundation for future investigations of photonic neural probe enabled microendoscopes for deep-brain fluorescence imaging in vivo.

Recording Quality Is Systematically Related to Electrode Impedance

Extracellular recordings with planar microelectrodes are the gold standard technique for recording the fast action potentials of neurons in the intact brain. The introduction of microfabrication techniques has revolutionized the in vivo recording of neuronal activity and introduced high-density, multi-electrode arrays that increase the spatial resolution of recordings and the number of neurons that can be simultaneously recorded. Despite these innovations, there is still debate about the ideal electrical transfer characteristics of extracellular electrodes. This uncertainty is partly due to the lack of systematic studies comparing electrodes with different characteristics, particularly for chronically implanted arrays over extended time periods. Here a high-density, flexible, and thin-film array is fabricated and tested, containing four distinct electrode types differing in surface material and surface topology and, thus, impedance. It is found that recording quality is strongly related to electrode impedance with signal amplitude and unit yield negatively correlated to impedance. Electrode impedances are stable for the duration of the experiment (up to 12 weeks) and recording quality does not deteriorate. The findings support the expectation from the theory that recording quality will increase as impedance decreases.

Revolutionizing Drug Delivery and Therapeutics: The Biomedical Applications of Conductive Polymers and Composites-Based Systems

The first conductive polymers (CPs) were developed during the 1970s as a unique class of organic substances with properties that are electrically and optically comparable to those of inorganic semiconductors and metals while also exhibiting the desirable traits of conventional polymers. CPs have become a subject of intensive research due to their exceptional qualities, such as high mechanical and optical properties, tunable electrical characteristics, ease of synthesis and fabrication, and higher environmental stability than traditional inorganic materials. Although conducting polymers have several limitations in their pure state, coupling with other materials helps overcome these drawbacks. Owing to the fact that various types of tissues are responsive to stimuli and electrical fields has made these smart biomaterials attractive for a range of medical and biological applications. For various applications, including the delivery of drugs, biosensors, biomedical implants, and tissue engineering, electrical CPs and composites have attracted significant interest in both research and industry. These bimodalities can be programmed to respond to both internal and external stimuli. Additionally, these smart biomaterials have the ability to deliver drugs in various concentrations and at an extensive range. This review briefly discusses the commonly used CPs, composites, and their synthesis processes. Further highlights the importance of these materials in drug delivery along with their applicability in various delivery systems.

Post-explant profiling of subcellular-scale carbon fiber intracortical electrodes and surrounding neurons enables modeling of recorded electrophysiology

Objective.Characterizing the relationship between neuron spiking and the signals that electrodes record is vital to defining the neural circuits driving brain function and informing clinical brain-machine interface design. However, high electrode biocompatibility and precisely localizing neurons around the electrodes are critical to defining this relationship.Approach.Here, we demonstrate consistent localization of the recording site tips of subcellular-scale (6.8µm diameter) carbon fiber electrodes and the positions of surrounding neurons. We implanted male rats with carbon fiber electrode arrays for 6 or 12+ weeks targeting layer V motor cortex. After explanting the arrays, we immunostained the implant site and localized putative recording site tips with subcellular-cellular resolution. We then 3D segmented neuron somata within a 50µm radius from implanted tips to measure neuron positions and health and compare to healthy cortex with symmetric stereotaxic coordinates.Main results.Immunostaining of astrocyte, microglia, and neuron markers confirmed that overall tissue health was indicative of high biocompatibility near the tips. While neurons near implanted carbon fibers were stretched, their number and distribution were similar to hypothetical fibers placed in healthy contralateral brain. Such similar neuron distributions suggest that these minimally invasive electrodes demonstrate the potential to sample naturalistic neural populations. This motivated the prediction of spikes produced by nearby neurons using a simple point source model fit using recorded electrophysiology and the mean positions of the nearest neurons observed in histology. Comparing spike amplitudes suggests that the radius at which single units can be distinguished from others is near the fourth closest neuron (30.7 ± 4.6µm,X-± S) in layer V motor cortex.Significance.Collectively, these data and simulations provide the first direct evidence that neuron placement in the immediate vicinity of the recording site influences how many spike clusters can be reliably identified by spike sorting.

A Review: Research Progress of Neural Probes for Brain Research and Brain-Computer Interface

Neural probes, as an invasive physiological tool at the mesoscopic scale, can decipher the code of brain connections and communications from the cellular or even molecular level, and realize information fusion between the human body and external machines. In addition to traditional electrodes, two new types of neural probes have been developed in recent years: optoprobes based on optogenetics and magnetrodes that record neural magnetic signals. In this review, we give a comprehensive overview of these three kinds of neural probes. We firstly discuss the development of microelectrodes and strategies for their flexibility, which is mainly represented by the selection of flexible substrates and new electrode materials. Subsequently, the concept of optogenetics is introduced, followed by the review of several novel structures of optoprobes, which are divided into multifunctional optoprobes integrated with microfluidic channels, artifact-free optoprobes, three-dimensional drivable optoprobes, and flexible optoprobes. At last, we introduce the fundamental perspectives of magnetoresistive (MR) sensors and then review the research progress of magnetrodes based on it.

Recent Advances in 3D Printing of Biomedical Sensing Devices

Additive manufacturing, also called 3D printing, is a rapidly evolving technique that allows for the fabrication of functional materials with complex architectures, controlled microstructures, and material combinations. This capability has influenced the field of biomedical sensing devices by enabling the trends of device miniaturization, customization, and elasticity (i.e., having mechanical properties that match with the biological tissue). In this paper, the current state-of-the-art knowledge of biomedical sensors with the unique and unusual properties enabled by 3D printing is reviewed. The review encompasses clinically important areas involving the quantification of biomarkers (neurotransmitters, metabolites, and proteins), soft and implantable sensors, microfluidic biosensors, and wearable haptic sensors. In addition, the rapid sensing of pathogens and pathogen biomarkers enabled by 3D printing, an area of significant interest considering the recent worldwide pandemic caused by the novel coronavirus, is also discussed. It is also described how 3D printing enables critical sensor advantages including lower limit-of-detection, sensitivity, greater sensing range, and the ability for point-of-care diagnostics. Further, manufacturing itself benefits from 3D printing via rapid prototyping, improved resolution, and lower cost. This review provides researchers in academia and industry a comprehensive summary of the novel possibilities opened by the progress in 3D printing technology for a variety of biomedical applications.

Scalable nanophotonic neural probes for multicolor and on-demand light delivery in brain tissue

Neural probes arein vivobrain-invasive devices that record and manipulate neural circuits using electricity, light, or drugs. The capability to shine distinct wavelengths and control their respective output locations for activation or deactivation of specific groups of neurons is desirable but remains unachieved. Here, we discuss our probe's capability to deliver two independently controllable wavelengths (450 and 655 nm) in the location(s) of interest using nanophotonic directional couplers and ring resonators. These nanophotonics are scalable to dozens of outputs without significantly increasing the device's lateral dimensions. Furthermore, they are entirely passive and thus do not require electrical input that results in heat generation. Besides, we integrate a high number of electrodes for a simultaneous neural activity readout. Thus, we overcome the challenges associated with multicolor illumination for neural devices by exploiting the capability of miniaturizable, passive probes to deliver two different frequencies in several areas of interest. These devices open the path towards investigating thein vivoelectrical signal propagation under the individual or simultaneous activation or inhibition of distinct brain regions.

In Vivo Photopharmacology Enabled by Multifunctional Fibers

Photoswitchable ligands can add an optical switch to a target receptor or signaling cascade and enable reversible control of neural circuits. The application of this approach, termed photopharmacology, to behavioral experiments has been impeded by a lack of integrated hardware capable of delivering both light and compounds to deep brain regions in moving subjects. Here, we devise a hybrid photochemical genetic approach to target neurons using a photoswitchable agonist of the capsaicin receptor TRPV1, red-AzCA-4. Using multifunctional fibers with optical and microfluidic capabilities, we delivered a transgene coding for TRPV1 into the ventral tegmental area (VTA). This sensitized excitatory VTA neurons to red-AzCA-4, allowing us to optically control conditioned place preference in mice, thus extending applications of photopharmacology to behavioral experiments. Applied to endogenous receptors, our approach may accelerate future studies of molecular mechanisms underlying animal behavior.

Bioinspired Materials for In Vivo Bioelectronic Neural Interfaces

The success of in vivo neural interfaces relies on their long-term stability and large scale in interrogating and manipulating neural activity after implantation. Conventional neural probes, owing to their limited spatiotemporal resolution and scale, face challenges for studying the massive, interconnected neural network in its native state. In this review, we argue that taking inspiration from biology will unlock the next generation of in vivo bioelectronic neural interfaces. Reducing the feature sizes of bioelectronic neural interfaces to mimic those of neurons enables high spatial resolution and multiplexity. Additionally, chronic stability at the device-tissue interface is realized by matching the mechanical properties of bioelectronic neural interfaces to those of the endogenous tissue. Further, modeling the design of neural interfaces after the endogenous topology of the neural circuitry enables new insights into the connectivity and dynamics of the brain. Lastly, functionalization of neural probe surfaces with coatings inspired by biology leads to enhanced tissue acceptance over extended timescales. Bioinspired neural interfaces will facilitate future developments in neuroscience studies and neurological treatments by leveraging bidirectional information transfer and integrating neuromorphic computing elements.

Ultra-small carbon fiber electrode recording site optimization and improved in vivo chronic recording yield

OBJECTIVE

Carbon fiber electrodes may enable better long-term brain implants, minimizing the tissue response commonly seen with silicon-based electrodes. The small diameter fiber may enable high-channel count brain-machine interfaces capable of reproducing dexterous movements. Past carbon fiber electrodes exhibited both high fidelity single unit recordings and a healthy neuronal population immediately adjacent to the recording site. However, the recording yield of our carbon fiber arrays chronically implanted in the brain typically hovered around 30%, for previously unknown reasons. In this paper we investigated fabrication process modifications aimed at increasing recording yield and longevity.

APPROACH

We tested a new cutting method using a 532nm laser against traditional scissor methods for the creation of the electrode recording site. We verified the efficacy of improved recording sites with impedance measurements and in vivo array recording yield. Additionally, we tested potentially longer-lasting coating alternatives to PEDOT:pTS, including PtIr and oxygen plasma etching. New coatings were evaluated with accelerated soak testing and acute recording.

MAIN RESULTS

We found that the laser created a consistent, sustainable 257 ± 13.8 µm2 electrode with low 1 kHz impedance (19 ± 4 kΩ with PEDOT:pTS) and low fiber-to-fiber variability. The PEDOT:pTS coated laser cut fibers were found to have high recording yield in acute (97% > 100 µV pp , N = 34 fibers) and chronic (84% > 100 µV pp , day 7; 71% > 100 µV pp , day 63, N = 45 fibers) settings. The laser cut recording sites were good platforms for the PtIr coating and oxygen plasma etching, slowing the increase in 1 kHz impedance compared to PEDOT:pTS in an accelerated soak test.

SIGNIFICANCE

We have found that laser cut carbon fibers have a high recording yield that can be maintained for over two months in vivo and that alternative coatings perform better than PEDOT:pTS in accelerated aging tests. This work provides evidence to support carbon fiber arrays as a viable approach to high-density, clinically-feasible brain-machine interfaces.

N3-MEA Probes: Scooping Neuronal Networks

In the current work, we introduce a brand new line of versatile, flexible, and multifunctional MEA probes, the so-called Nano Neuro Net, or N³-MEAs. Material choice, dimensions, and room for further upgrade, were carefully considered when designing such probes in order to cover the widest application range possible. Proof of the operation principle of these novel probes is shown in the manuscript via the recording of extracellular signals, such as action potentials and local field potentials from cardiac cells and retinal ganglion cells of the heart tissue and eye respectively. Reasonably large signal to noise ratio (SNR) combined with effortless operation of the devices, mechanical and chemical stability, multifunctionality provide, in our opinion, an unprecedented blend. We show successful recordings of (1) action potentials from heart tissue with a SNR up to 13.2; (2) spontaneous activity of retinal ganglion cells with a SNR up to 12.8; and (3) local field potentials with an ERG-like waveform, as well as spiking responses of the retina to light stimulation. The results reveal not only the multi-functionality of these N³-MEAs, but high quality recordings of electrogenic tissues.

Microfabricated Probes for Studying Brain Chemistry: A Review

Probe techniques for monitoring in vivo chemistry (e.g., electrochemical sensors and microdialysis sampling probes) have significantly contributed to a better understanding of neurotransmission in correlation to behaviors and neurological disorders. Microfabrication allows construction of neural probes with high reproducibility, scalability, design flexibility, and multiplexed features. This technology has translated well into fabricating miniaturized neurochemical probes for electrochemical detection and sampling. Microfabricated electrochemical probes provide a better control of spatial resolution with multisite detection on a single compact platform. This development allows the observation of heterogeneity of neurochemical activity precisely within the brain region. Microfabricated sampling probes are starting to emerge that enable chemical measurements at high spatial resolution and potential for reducing tissue damage. Recent advancement in analytical methods also facilitates neurochemical monitoring at high temporal resolution. Furthermore, a positive feature of microfabricated probes is that they can be feasibly built with other sensing and stimulating platforms including optogenetics. Such integrated probes will empower researchers to precisely elucidate brain function and develop novel treatments for neurological disorders.

Recent Progress of Development of Optogenetic Implantable Neural Probes

As a cell type-specific neuromodulation method, optogenetic technique holds remarkable potential for the realisation of advanced neuroprostheses. By genetically expressing light-sensitive proteins such as channelrhodopsin-2 (ChR2) in cell membranes, targeted neurons could be controlled by light. This new neuromodulation technique could then be applied into extensive brain networks and be utilised to provide effective therapies for neurological disorders. However, the development of novel optogenetic implants is still a key challenge in the field. The major requirements include small device dimensions, suitable spatial resolution, high safety, and strong controllability. In this paper, I present a concise review of the significant progress that has been made towards achieving a miniaturised, multifunctional, intelligent optogenetic implant. I identify the key limitations of current technologies and discuss the possible opportunities for future development.

Polymer Composite with Carbon Nanofibers Aligned during Thermal Drawing as a Microelectrode for Chronic Neural Interfaces

Microelectrodes provide a direct pathway to investigate brain activities electrically from the external world, which has advanced our fundamental understanding of brain functions and has been utilized for rehabilitative applications as brain-machine interfaces. However, minimizing the tissue response and prolonging the functional durations of these devices remain challenging. Therefore, the development of next-generation microelectrodes as neural interfaces is actively progressing from traditional inorganic materials toward biocompatible and functional organic materials with a miniature footprint, good flexibility, and reasonable robustness. In this study, we developed a miniaturized all polymer-based neural probe with carbon nanofiber (CNF) composites as recording electrodes via the scalable thermal drawing process. We demonstrated that in situ CNF unidirectional alignment can be achieved during the thermal drawing, which contributes to a drastic improvement of electrical conductivity by 2 orders of magnitude compared to a conventional polymer electrode, while still maintaining the mechanical compliance with brain tissues. The resulting neural probe has a miniature footprint, including a recording site with a reduced size comparable to a single neuron and maintained impedance that was able to capture neural activities. Its stable functionality as a chronic implant has been demonstrated with the long-term reliable electrophysiological recording with single-spike resolution and the minimal tissue response over the extended period of implantation in wild-type mice. Technology developed here can be applied to basic chronic electrophysiological studies as well as clinical implementation for neuro-rehabilitative applications.

Syringe-injectable mesh electronics integrate seamlessly with minimal chronic immune response in the brain

Implantation of electrical probes into the brain has been central to both neuroscience research and biomedical applications, although conventional probes induce gliosis in surrounding tissue. We recently reported ultraflexible open mesh electronics implanted into rodent brains by syringe injection that exhibit promising chronic tissue response and recording stability. Here we report time-dependent histology studies of the mesh electronics/brain-tissue interface obtained from sections perpendicular and parallel to probe long axis, as well as studies of conventional flexible thin-film probes. Confocal fluorescence microscopy images of the perpendicular and parallel brain slices containing mesh electronics showed that the distribution of astrocytes, microglia, and neurons became uniform from 2-12 wk, whereas flexible thin-film probes yield a marked accumulation of astrocytes and microglia and decrease of neurons for the same period. Quantitative analyses of 4- and 12-wk data showed that the signals for neurons, axons, astrocytes, and microglia are nearly the same from the mesh electronics surface to the baseline far from the probes, in contrast to flexible polymer probes, which show decreases in neuron and increases in astrocyte and microglia signals. Notably, images of sagittal brain slices containing nearly the entire mesh electronics probe showed that the tissue interface was uniform and neurons and neurofilaments penetrated through the mesh by 3 mo postimplantation. The minimal immune response and seamless interface with brain tissue postimplantation achieved by ultraflexible open mesh electronics probes provide substantial advantages and could enable a wide range of opportunities for in vivo chronic recording and modulation of brain activity in the future.

Optogenetics, Tools and Applications in Neurobiology

Comprehension of the brain function can be helpful for therapy of neurodegenerative diseases. The brain consists of various types of neuron sets, which organize in three-dimensional complex networks and form neural circuits underlying different behaviors. The circuits act based on the patterns that encode the brain functions. Recognition of the neural patterns requires methods to manipulate the neurons. Electrical stimulation may be the most common method. However, it has significant drawbacks including failure to identify specific neurons in experiments. As an alternative, optical stimulation is a new method that acts in combination with genetic approaches. The novel, optogenetic technology makes it feasible to manipulate either the specific cell types or the neural circuits. This is associated with minimum tissue damages as well as side effects. In this study, a new technology has been introduced, and then its optical and genetical tools have been investigated.

Flexible and stretchable nanowire-coated fibers for optoelectronic probing of spinal cord circuits

Studies of neural pathways that contribute to loss and recovery of function following paralyzing spinal cord injury require devices for modulating and recording electrophysiological activity in specific neurons. These devices must be sufficiently flexible to match the low elastic modulus of neural tissue and to withstand repeated strains experienced by the spinal cord during normal movement. We report flexible, stretchable probes consisting of thermally drawn polymer fibers coated with micrometer-thick conductive meshes of silver nanowires. These hybrid probes maintain low optical transmission losses in the visible range and impedance suitable for extracellular recording under strains exceeding those occurring in mammalian spinal cords. Evaluation in freely moving mice confirms the ability of these probes to record endogenous electrophysiological activity in the spinal cord. Simultaneous stimulation and recording is demonstrated in transgenic mice expressing channelrhodopsin 2, where optical excitation evokes electromyographic activity and hindlimb movement correlated to local field potentials measured in the spinal cord.

Highly Crumpled All-Carbon Transistors for Brain Activity Recording

Neural probes based on graphene field-effect transistors have been demonstrated. Yet, the minimum detectable signal of graphene transistor-based probes is inversely proportional to the square root of the active graphene area. This fundamentally limits the scaling of graphene transistor-based neural probes for improved spatial resolution in brain activity recording. Here, we address this challenge using highly crumpled all-carbon transistors formed by compressing down to 16% of its initial area. All-carbon transistors, chemically synthesized by seamless integration of graphene channels and hybrid graphene/carbon nanotube electrodes, maintained structural integrity and stable electronic properties under large mechanical deformation, whereas stress-induced cracking and junction failure occurred in conventional graphene/metal transistors. Flexible, highly crumpled all-carbon transistors were further verified for in vivo recording of brain activity in rats. These results highlight the importance of advanced material and device design concepts to make improvements in neuroelectronics.

A National Network of Neurotechnology Centers for the BRAIN Initiative

We propose the creation of a national network of neurotechnology centers to enhance and accelerate the BRAIN Initiative and optimally leverage the effort and creativity of individual laboratories involved in it. As "brain observatories," these centers could provide the critical interdisciplinary environment both for realizing ambitious and complex technologies and for providing individual investigators with access to them.

Bridging the Divide between Neuroprosthetic Design, Tissue Engineering and Neurobiology

Neuroprosthetic devices have made a major impact in the treatment of a variety of disorders such as paralysis and stroke. However, a major impediment in the advancement of this technology is the challenge of maintaining device performance during chronic implantation (months to years) due to complex intrinsic host responses such as gliosis or glial scarring. The objective of this review is to bring together research communities in neurobiology, tissue engineering, and neuroprosthetics to address the major obstacles encountered in the translation of neuroprosthetics technology into long-term clinical use. This article draws connections between specific challenges faced by current neuroprosthetics technology and recent advances in the areas of nerve tissue engineering and neurobiology. Within the context of the device-nervous system interface and central nervous system implants, areas of synergistic opportunity are discussed, including platforms to present cells with multiple cues, controlled delivery of bioactive factors, three-dimensional constructs and in vitro models of gliosis and brain injury, nerve regeneration strategies, and neural stem/progenitor cell biology. Finally, recent insights gained from the fields of developmental neurobiology and cancer biology are discussed as examples of exciting new biological knowledge that may provide fresh inspiration toward novel technologies to address the complexities associated with long-term neuroprosthetic device performance.