Adaptive frequency-domain filtering for neural signal preprocessing.

Electrical interference from various sources is a common issue for experimental extracellular electrophysiology recordings collected using multi-electrode array neural recording systems. This interference deteriorates the signal-to-noise ratio (SNR) of the raw electrophysiology signals and hampers the accuracy of data post-processing using techniques such as spike-sorting. Traditional signal processing methods to digitally remove electrical interference during post-processing include bandpass filtering to limit the signal to the relevant spectral range of the biological data, e.g., the spikes band (300 Hz - 7 kHz), targeted notch filtering to remove power line interference from standard alternating current mains electricity and common reference removal to minimize noise common to all electrodes. These methods require a priori knowledge of the frequency of the interfering signal source to address the unique electromagnetic interference environment of each experimental setup. We discuss an adaptive method for automatically removing narrow-band electrical interference through a spectral peak detection and removal (SPDR) step that can be applied during post-processing of the recorded data, based on the intuition that tall, narrowband signals localized in the signal spectrum correspond to interference, rather than the activity of neurons. A spectral peak prominence (SPP) threshold is used to detect these peaks in the frequency domain, which will then be removed via notch filtering. We applied this method to simulated waveforms and also experimental electrophysiology data collected from cerebral organoids to demonstrate its effectiveness for removing unwanted interference without significantly distorting the neural signals. We discuss that proper selection of the SPP threshold is required to avoid over-filtering, which can result in distortion of the electrophysiology data. We also compare the firing-rate activity in the filtered electrophysiology with fluorescence calcium imaging, a secondary cellular activity marker, to quantify signal distortion and provide bounds on SNR-based optimization of the SPP threshold. The adaptive filtering technique demonstrated in this paper is a powerful method that can automatically detect and remove interband interference in recorded neural signals, potentially enabling data collection in more naturalistic settings where external interference signals are difficult to eliminate.

2D optical confinement in an etchless stratified trench waveguide.

We demonstrate novel trapezoidal and rectangular stratified trench optical waveguide designs that feature low-loss two-dimensional confinement of guided optical modes that can be realized in continuous polymer thin film layers formed in a trench mold. The design is based on geometrical bends in a thin film core to enable two-dimensional confinement of light in the transverse plane, without any variation in the core thickness. Incidentally, the waveguide design would completely obviate the need for etching the waveguide core, avoiding the scattering loss due to the etched sidewall roughness. This new design exhibits an intrinsic leakage loss due to coupling of light out of the trench, which can be minimized by choosing an appropriate waveguide geometry. Finite-difference eigenmode simulation demonstrates a low intrinsic leakage loss of less than 0.15 dB/cm. We discuss the principle of operation of these stratified trench waveguides and present the design and numerical simulations of a specific realization of this waveguide geometry. The design considerations and tradeoffs in propagation loss and confinement compared with traditional ridge waveguides are discussed.

Low-loss flexible Parylene photonic waveguides for optical implants.

We demonstrate compact, low-loss (<5 dB/cm) Parylene C photonic waveguides in a flexible, biocompatible, all-polymer platform suitable for implantable applications. The scattering loss due to the sidewall roughness resulting from the reactive ion etching of Parylene C was identified as the primary source of propagation loss. A fabrication process utilizing the conformal coating of Parylene C was developed to significantly reduce waveguide propagation loss (by more than 30 dB/cm). We also performed thermal annealing at 300°C to smoothen the sidewalls; however, it was found to adversely affect the waveguide performance.

CMU Array: A 3D nanoprinted, fully customizable high-density microelectrode array platform.

Microelectrode arrays provide the means to record electrophysiological activity critical to brain research. Despite its fundamental role, there are no means to customize electrode layouts to address specific experimental or clinical needs. Moreover, current electrodes demonstrate substantial limitations in coverage, fragility, and expense. Using a 3D nanoparticle printing approach that overcomes these limitations, we demonstrate the first in vivo recordings from electrodes that make use of the flexibility of the 3D printing process. The customizable and physically robust 3D multi-electrode devices feature high electrode densities (2600 channels/cm2 of footprint) with minimal gross tissue damage and excellent signal-to-noise ratio. This fabrication methodology also allows flexible reconfiguration consisting of different individual shank lengths and layouts, with low overall channel impedances. This is achieved, in part, via custom 3D printed multilayer circuit boards, a fabrication advancement itself that can support several biomedical device possibilities. This effective device design enables both targeted and large-scale recording of electrical signals throughout the brain.

A Semi-Automated System for Wafer-Scale Optical Waveguide Characterization.

Integrated photonic waveguide systems are used in biomedical sensing and require robust, high-throughput methods of characterization. Here, we demonstrate a semi-automated robotic system to characterize waveguides at the wafer-scale with minimal human intervention based on imaging the outscattered light to measure the propagation loss. We demonstrate automated input coupling efficiency optimization using closed-loop control of the input fiber position. The automated characterization system collects and combines multiple images of the waveguide to measure the propagation loss. This system allows high-throughput characterization of integrated photonic waveguides and lays the foundation for a fully automated and high throughput system to characterize photonic waveguides at the wafer scale.Clinical Relevance- This method enables high precision, high throughput characterization of optoelectrical neural probes to maximize the yield of surgical implantation and electrophysiology recording.

Parylene Photonic Microimager for Implantable Imaging.

We have recently introduced a fully flexible, compact photonic platform, Parylene photonics. Here, we demonstrate a Parylene photonic waveguide array microimager with a light source localization accuracy of 17.04 µm along the x-axis and 30.07 µm along the y-axis over a 200 µm×1000 µm region. We show the feasibility of fluorescent imaging from mouse brain tissue using the microimager array.Clinical Relevance- Implantable microimagers can be used for clinical intraoperative monitoring as well as structural and functional imaging with cell-type specificity in research.

Bioelectrical interfaces with cortical spheroids in three-dimensions.

Objective.Three-dimensional (3D) neuronal spheroid culture serves as a powerful model system for the investigation of neurological disorders and drug discovery. The success of such a model system requires techniques that enable high-resolution functional readout across the entire spheroid. Conventional microelectrode arrays and implantable neural probes cannot monitor the electrophysiology (ephys) activity across the entire native 3D geometry of the cellular construct.Approach.Here, we demonstrate a 3D self-rolled biosensor array (3D-SR-BA) integrated with a 3D cortical spheroid culture for simultaneousin vitroephys recording, functional Ca2+imaging, while monitoring the effect of drugs. We have also developed a signal processing pipeline to detect neural firings with high spatiotemporal resolution from the ephys recordings based on established spike sorting methods.Main results.The 3D-SR-BAs cortical spheroid interface provides a stable, high sensitivity recording of neural action potentials (<50µV peak-to-peak amplitude). The 3D-SR-BA is demonstrated as a potential drug screening platform through the investigation of the neural response to the excitatory neurotransmitter glutamate. Upon addition of glutamate, the neural firing rates increased notably corresponding well with the functional Ca2+imaging.Significance.Our entire system, including the 3D-SR-BA integrated with neuronal spheroid culture, enables simultaneous ephys recording and functional Ca2+imaging with high spatiotemporal resolution in conjunction with chemical stimulation. We demonstrate a powerful toolset for future studies of tissue development, disease progression, and drug testing and screening, especially when combined with native spheroid cultures directly extracted from humans.

Flexible optoelectric neural interfaces.

Understanding the neural basis of brain function and dysfunction and designing effective therapeutics require high resolution targeted stimulation and recording of neural activity. Optical methods have been recently developed for neural stimulation as well as functional and structural imaging. These methods call for implantable devices to deliver light into the neural tissue at depth with high spatiotemporal resolution. To address this need, rigid and flexible neurophotonic implants have been recently designed. This article reviews the state-of-the-art flexible passive and active penetrating optical neural probes developed for light delivery with minimal damage to the tissue. Passive and active flexible neurophotonic implants are compared and insights about future directions are provided.

Parylene photonics: a flexible, broadband optical waveguide platform with integrated micromirrors for biointerfaces.

Targeted light delivery into biological tissue is needed in applications such as optogenetic stimulation of the brain and in vivo functional or structural imaging of tissue. These applications require very compact, soft, and flexible implants that minimize damage to the tissue. Here, we demonstrate a novel implantable photonic platform based on a high-density, flexible array of ultracompact (30 µm × 5 µm), low-loss (3.2 dB/cm at λ = 680 nm, 4.1 dB/cm at λ = 633 nm, 4.9 dB/cm at λ = 532 nm, 6.1 dB/cm at λ = 450 nm) optical waveguides composed of biocompatible polymers Parylene C and polydimethylsiloxane (PDMS). This photonic platform features unique embedded input/output micromirrors that redirect light from the waveguides perpendicularly to the surface of the array for localized, patterned illumination in tissue. This architecture enables the design of a fully flexible, compact integrated photonic system for applications such as in vivo chronic optogenetic stimulation of brain activity.

High Density, Double-Sided, Flexible Optoelectronic Neural Probes With Embedded µLEDs.

Optical stimulation and imaging of neurons deep in the brain require implantable optical neural probes. External optical access to deeper regions of the brain is limited by scattering and absorption of light as it propagates through tissue. Implantable optoelectronic probes capable of high-resolution light delivery and high-density neural recording are needed for closed-loop manipulation of neural circuits. Micro-light-emitting diodes (µLEDs) have been used for optical stimulation, but predominantly on rigid silicon or sapphire substrates. Flexible polymer neural probes would be preferable for chronic applications since they cause less damage to brain tissue. Flexible µLED neural probes have been recently implemented by flip-chip bonding of commercially available µLED chips onto flexible substrates. Here, we demonstrate a monolithic design for flexible optoelectronic neural interfaces with embedded gallium nitride µLEDs that can be microfabricated at wafer-scale. Parylene C is used as the substrate and insulator due to its biocompatibility, compliance, and optical transparency. We demonstrate one-dimensional and two-dimensional individually-addressable µLED arrays. Our µLEDs have sizes as small as 22 × 22 µm in arrays of up to 32 µLEDs per probe shank. These devices emit blue light at a wavelength of 445 nm, suitable for stimulation of channelrhodopsin-2, with output powers greater than 200 µW at 2 mA. Our flexible optoelectronic probes are double-sided and can illuminate brain tissue from both sides. Recording electrodes are co-fabricated with µLEDs on the front- and backside of the optoelectronic probes for electrophysiology recording of neuronal activity from the volumes of tissue on the front- and backside simultaneously with bi-directional optical stimulation.