This PDF file contains the front matter associated with SPIE Proceedings Volume 11663, including the Title Page, Copyright information, and Table of Contents.

Introduction to SPIE Photonics West BiOS conference 11663: Integrated Sensors for Biological and Neural Sensing

Optogenetics is a powerful tool for relating brain function to behavior, as it enables cell-type specific manipulation and recording of neurons with high spatial and temporal precision. Although optogenetics has been used successfully in nonhuman primates, reliable techniques had not been developed for large-scale, bi-directional study of neural circuits in these animals. Here we present practical and stable interfaces for stimulation and recording of large-scale cortical circuits. To obtain optogenetic expression across a broad region, spanning large cortical areas (5 cm2 ), we used convection-enhanced delivery of the viral vector, with online guidance from magnetic resonance imaging. To record neural activity across this region, we used micro-electrocorticographic (μECoG) arrays designed to minimally attenuate optical stimuli. Lastly, we have incorporated the capability of producing focal and modular photochemical ischemic lesions in these interfaces enabling us to stimulate the cortex around the site of injury and monitor functional recovery via change in blood flow, neurophysiology and behavior. These interfaces offer powerful tools for studying circuit dynamics and connectivity across cortical areas, for long-term studies of neuromodulation, and for linking these to behavior. Currently we are using these technologies towards developing therapeutic interventions for neurological disorders such as stroke.

With the advent of optical methods for stimulation and functional recording of neuronal activity in the brain, there is a growing need for fully flexible, ultracompact photonic devices for light delivery and light collection in brain tissue. In this paper, we will discuss our recent advances in designing a flexible optoelectronic neural implant platform that integrates passive and active optical components with electrical recording functionality. We leverage the exquisite optical and electrical insulation properties Parylene C, a biocompatible and flexible polymer to realize a fully functional optoelectrical neural interface.

We developed multi-modal systems comprising implantable carbon fiber (CF)-based electrodes to record synchronously chemical (e.g. dopamine) and electrical (e.g. local field potential, LFP) forms of activity in the brain. These systems were equipped with implantable micro-invasive probes and moveable silica-based CF probes capable of recording chronically from fixed locations, or from multiple depths along predetermined trajectories, respectively, spanning 48 spatially distinct sites in the caudate nucleus and the putamen. Electrochemical fast scan cyclic voltammetry (FSCV) was implemented in combination with standard electrophysiology to provide subsecond chemical and electrical recordings. The chronic stability of our micro-invasive probes, as tested previously in rodents and translated for use in nonhuman primate (NHP), was necessary to ensure functional recording from fixed locations in the brain without degradation in probe sensitivity over time. These systems were used to examine the relationship between dopamine and beta-band LFPs, prominent biomarkers of untreated Parkinson’s disease. We recorded dopamine and beta in rhesus monkeys performing oculomotor tasks in which reward valuation and movement control, key functions impaired in Parkinson’s disease, could be quantified. Highly stable measurements of dopamine and LFP neural signals were made over a period of months.

Advanced electronic/optoelectronic systems that enable intimate integration with soft tissues of the brain, the spinal cord and the peripheral nerves will accelerate progress in neuroscience research; they will also serve as the foundations for new approaches in regenerative medicine and in the treatment of neurodegenerative disease. Specifically, capabilities for injecting miniaturized electronic elements, light sources, photodetectors, multiplexed sensors, programmable microfluidic networks and other components into precise locations of the deep brain or for softly laminating them onto the surfaces of peripheral nerves will open up unique and important opportunities in stimulating, inhibiting and monitoring neural circuit behaviors. This presentation describes concepts in materials science and assembly processes that underpin these types of technologies.

Action potentials generated by motor neurons in the brain and spinal cord carry information about intended and ongoing movement. These biopotentials are typically measured with sensors placed in close proximity to the neurons, providing a direct readout of motor output. For people that have become paralyzed due to spinal cord injury, such readouts can be used to form control signals for operating assistive devices, such as robotic arms and exoskeletons. While most methods for measuring the firing activity of single neurons rely on electrodes that are implanted in the brain, the requirement for surgery poses a barrier to widespread use. Here, we demonstrate that a wearable sensor array can detect residual motor unit activity in muscles paralyzed after severe cervical spinal cord injury. Despite generating no observable hand movement, the volitional recruitment of motor neurons below the level of injury was observed across attempted movements of individual fingers and overt wrist and elbow movements. Subgroups of motor units were coactive during flexion or extension phases of the task. Single digit movement intentions were classified offline from the EMG power (root-mean-square) or motor unit firing rates. Median classification accuracy was 76% when using the root-mean-square of the EMG and 76.5% when using motor unit firing rates. This study provides the first demonstration of a wearable interface for recording and decoding firing rates of motor neurons below the level of spinal cord injury.

Time-Domain Near-Infrared Spectroscopy (TD-NIRS) has been considered as the gold standard of non-invasive optical brain imaging devices. However, due to the high cost, complexity, and large form-factor, it has not been as widely adopted as Continuous Wave (CW) NIRS systems. Kernel Flow is a TD-NIRS system that has been designed to break through these limitations by maintaining the performance of a research grade TD-NIRS system while integrating all of the components into a small modular device. The Kernel Flow modules are built around miniaturized laser drivers, custom integrated circuits, and specialized detectors. The modules can be assembled into a system with dense channel coverage over the entire head. We show performance similar to benchtop systems with our miniaturized device.

Steady cerebral blood flow (CBF) is needed for normal brain function, but continuous monitoring of CBF in humans is currently challenging. Here, by leveraging a low-cost sensor technology, we introduce a class of novel near-infrared optical devices that monitor CBF continuously and non-invasively in adult humans. We achieve this by replacing expensive single photon counting detectors, currently used for optical CBF monitors, with complementary metal–oxide–semiconductor (CMOS) arrays. We maintain performance by employing an additional optical “trick” known as interferometry, which transforms each CMOS pixel into a sensitive detector for fluctuations of coherent light that probes blood flow in the brain. Our method is called interferometric Diffusing Wave Spectroscopy (iDWS). In this talk we describe technical advantages of iDWS, including recent advances in our approach, and broadly envisage how interferometry can help to advance the field of diffuse optical brain monitoring.

My research group strives to address unmet clinical needs by creating tailorable three-dimensional free-form electronics and biomedical devices with 3D printing technologies. As an example, I will highlight the development of 3D printed quantum-dots light-emitting diode, which extended the reach of 3D printing and demonstrated that active electronic materials and devices can be entirely 3D printed. I will then highlight the latest development of a 3D printed gastric resident electronics system, which leverages the significant space and immune-tolerant environment available within the gastrointestinal tract to circumvent the potential complications associated with surgically placed medical implants.

Novel concepts of vibrational spectroscopic sensors for biophotonic applications are introduced: (I) Raman point-of-care sensors for microbial analysis (e.g. rapid detection of pathogens and their antibiotic resistance pattern together with host response, detection of pathogens in food); (II) cavity enhanced and fiber enhanced Raman sensors for on-site environmental and drug monitoring; (III) linear and non-linear Raman fiber probes for intraoperative histopathological tissue screening; (IV) surface enhanced Raman spectroscopy (SERS) and surface enhanced IR absorption (SEIRA) sensors for ultrasensitive bio analysis (e.g. detection of antibiotics or disease metabolites in body liquids, forbidden substances in food or metamaterial concepts for chiral biosensing).

Imaging has become one of the most important tools for categorizing neurons based on their function. However, for a cell type identified only by its pattern of activity, the process of identifying molecular markers remains laborious. We developed physiological optical tagging sequencing (PhOTseq), a technique for tagging and expression profiling of cells on the basis of their functional properties. We developed a reporter combining a green calcium indicator (GCaMP) with a photoactivatable red reporter (PAmCherry). When visualizing neuronal activity in such animals, real-time analysis allowed digital selection of cells exhibiting specific activity patterns, and photoactivation was directed specifically to those cells to tag them for later harvesting and analysis. We found that PhOTseq was capable of selecting rare cell types and enriching them by nearly 100-fold. We applied PhOTseq to the challenge of mapping receptor-ligand pairings among pheromone-sensing neurons in mice, and densely mapped the cell types responsible for encoding a specific portion of the sensory world.

We provide an overview of some of our recent work on the use of deep neural networks in advancing computational microscopy and sensing systems, also covering their biomedical applications.

Newly demonstrated advanced biosensor imaging technologies utilize the unique electromagnetic capabilities of photonic metamaterials to enhance the interaction between light and biological matter. The resulting capabilities address gaps in existing technologies for biomolecular analysis that rely upon enzymatic and chemical amplification, costly instrumentation, and complex assay protocols. Through amplification of the excitation/extraction efficiency of light emitting tags, absorption efficiency of nanoparticle tags, and scattering efficiency of biological analytes, technology platforms have been demonstrated that are capable of ultrasensitive, digital-resolution, room temperature, isothermal, rapid, and highly quantitative biomolecular analysis.

The interfacing of electronics with biology is a rapidly growing field fueled by the development of new materials and devices. Along this direction, organic electrochemical transistors (OECTs) are triggering increasing attention and several bioelectronic applications have been demonstrated. OECTs provide bulk volumetric ionic-electronic coupling, thus enabling the seamless integration of bioelectronic. Here, starting from the OECT fundamentals, OECT-based integrated sensor architectures for enhanced and multifunctional ionic-to-electronic transduction and amplification are presented and discussed. Then, the concepts of local transduction and amplification as well as multiscale and reconfigurable sensor operations are presented and discussed. Finally, guidelines useful for the design of high-sensitivity OECT-based integrated bioelectronic sensors are provided.

Magnetic detection in PCR relies on giant magnetoresistive (GMR) sensors whose resistance depends on the magnetic field. Thus, a bound sample that is also bound to a magnetic nanoparticle can be detected magnetically because of the effect of the magnetic nanoparticle on the nearby magnetic field. However, the resistance of GMR sensors also depends on their temperature, posing a unique challenge to the integration of PCR with GMR sensors on a single chip. Here we report accurate control and measurement of temperature in GMR detection for PCR assays and multiplexed DNA biomarker detection for point of care testing (POCT). In particular, GMR biosensors integrated with PCR are extremely promising as a POCT for therapy monitoring of lung cancer management.

Gastric contractions are coordinated by an underlying bioelectrical activity, termed slow waves. Aberrant slow-wave patterns have been associated with gastric dysmotility. High-resolution mapping of slow waves has potential to detect the mechanisms underlying gastric dysrhythmias. I will present our recent efforts towards the development of wireless implantable systems for gastric slow-wave recording. First, an inductively powered implantable system will be presented along with its shortcomings. Then, a new paradigm will be presented for large-scale gastric interfacing by developing a network of distributed, miniaturized, ultrasonically interrogated implants. Finally, the concept of a new technique for robust ultrasonic beamforming will be presented.

In this presentation, we will present a general biosensor technology capable of continuously tracking a wide range of molecules in living subjects. Our real-time biosensor requires no exogenous reagents and can be readily reconfigured to measure different target molecules by exchanging molecular probes in a modular manner. Next, we will present the first real-time, closed loop feedback control of drug concentration in live animals using the real-time biosensor and discuss potential applications of our technology. Finally, we will discuss methods for generating synthetic molecular switches that are at the heart of the biosensor.

Macular degeneration leads to blindness due to loss of the “image capturing” photoreceptors, while neurons in the “image-processing” inner retinal layers are relatively well preserved. Photovoltaic subretinal prosthesis converts light into pulsed electric current, stimulating the nearby inner retinal neurons. Clinical trial with such implants having 100um pixels, as well as preclinical measurements with 75 and 55um pixels, confirm that spatial resolution of prosthetic vision can reach the pixel pitch. For a broad acceptance of this technology, visual acuity should exceed 20/100, which requires pixels smaller than 25um. I will present 3-dimensional electro-neural interface scalable down to cellular-scale pixel size.

Microflow cytometry has become an attractive tool for counting and analysis of complex cell population and finds many applications in life science research. However, its implementation in screening small sized targets, such as microorganisms, is limited by challenges associated with sample handling and detection in a flow. Here, we report the function of a 3D flow focusing microfluidic system as a high performance, multi-parameter flow cytometry. The system consists of a detection chamber that can precisely control a highly focused sample flow in 3D and an integrated optical fiber to collect the scattered light at the vertical plane. The ability of the system to detect small beads (1 µm), differentiate subtle differences (2 µm) and accurately profile a mixed bead population is demonstrated. Furthermore, multiple types of information about the sample, including the inherent biochemical information (e.g., fluorescence or Raman signal) and physical properties (e.g., size) are simultaneously generated, allowing sophisticated cellular analysis. Together with the facile and robust operation, this provides a versatile tool that could be used for multi-parametric analyses in a diversity of applications.

Protein phosphorylation is responsible for a broad range of signal transduction roles such as muscular movement and growth, metastatic behavior, mental cognition and metabolic rate. This process follows an enzymatic reaction mechanism, where the enzyme or kinase facilitates the transfer of the phosphate group from adenosine triphosphate (ATP) to the substrate protein. To better understand signal transduction, we designed and fabricated microfluidic devices, integrated them with our confocal Raman spectrometer, and monitored real time signal changes from ATP. In this study, we loaded the microfluidic device with Casein in MgCl2 solution, and fed into the chamber a solution of PKA/cAMP/ATP in MgCl2 using Tygon tubing attached to 1 ml syringes with 30g needles attached. At time, t=0, the reactor is preloaded with the Casein MgCl2 solution, and ATP is absent from the chamber. The PKA/cAMP/ATP in MgCl2 solution was allowed to flow at a rate of 0.005 mg/min until the POx peaks between 1000-1600 /cm appeared in the Raman spectra. At this point, the fluid flow was stopped and the reaction progressed while Raman spectra was collected over the wavenumber range 1000 – 1600 /cm to monitor phosphate bonds. Results align with calculations from mass transfer analysis. The isoelectric point of phosphorylated Casein, dephosphorylated Casein, and PKA as reported from literature [1] were observed from the reaction performed in the microfluidic reactor. This confirmed real time observation of phosphorylation of Casein through catalysis of PKA and phosphate donation from ATP.

We modeled and conducted microfluidic device reaction experiments to evaluate mass transfer of enzymes during protein phosphorylation to better understand signal transduction. In this work, we studied the effects of fluid flow rates in our microfluidic device, where molecular arrangements were monitored using a modular confocal Raman system. We focused on the phosphate bond since this resulted in the greatest source of signal variance in both solid- and solution-based experiments. We performed initial measurements that eliminate instrumental effects and conducted flow experiments that correlate phosphate intensities to water flow rates. We also studied flow of varying concentrations of adenosine triphosphate (ATP) and adenosine diphosphate (ADP), tracked the phosphate modes that appear between 1000-1600 /cm and based on these measurements, confirmed when the chamber transitions from ATP to ADP. By doing so, this study provides evidence that monitoring in real time and non-invasively the transition from ATP to ADP within the microfluidic chamber is achievable and enables the study of protein phosphorylation events.

To use optical techniques deep in tissue, implantable microdevices which can collect and deliver light with high efficiency are needed. Flexible polymer devices can reduce tissue damage. Here, we demonstrate a fully-flexible, low-loss (3.2 dB/cm @ 680 nm), broadband (450-680 nm) integrated photonic platform composed entirely of Parylene C and PDMS. Using this platform, we demonstrate devices with an array of 6 waveguides and 1.3 cm total length. We integrate bare laser diode chips (220 x 220 μm, λ= 680 nm) to realize a light delivery system for optogenetics. Simulation, characterization, and biological demonstration will be discussed.

Ions are fundamental biological regulators enabling the communication between cells, regulating metabolic and bioenergetic processing and playing a key role in pH regulation and hydration. The in-situ quantification of the ion concentration is gathering relevant interest in biomedical diagnostics and healthcare. State-of-art transistor-based ion sensors show an intrinsic trade-off between sensitivity, operating range and supply voltage. To overcome these limitations, here we focus on ion sensor amplifiers where complementary OECTs are integrated in a push-pull configuration, providing sensitivity larger than 1 V/dec at a supply voltage down to 0.5 V and operating in the physiological range. Ion detection over a range of five orders of magnitude and real-time monitoring of variations two orders of magnitude lower than the detected concentration are achieved. The ion-sensitive amplifier sets a new benchmark for ion-sensing devices, opening possibilities for predictive diagnostics and personalized medicine.

Morphine is an analgesic narcotic drug with a high risk for addiction. Testing standards require urine samples processed by central laboratories, leading to delayed results. Giant magnetoresistive sensors coupled with super paramagnetic nanoparticles offer a quantitative, sensitive, and low-cost solution for morphine detection in saliva at the point of care. The smartphone-controlled platform transmits results via Bluetooth, takes 35 minutes from sample to result, and delivers a lower limit of detection of 3.78 ng/mL and a dynamic range up to 500 ng/mL. The affordable and multiplexable GMR nanosensor platform enables this technology to be widely utilized for workplace drug testing.