Implantable photonic neural probes for light-sheet fluorescence brain imaging

Implantable silicon neural probes with nanophotonic phased arrays for single-lobe beam steering

In brain activity mapping with optogenetics, patterned illumination is crucial for targeted neural stimulation. However, due to optical scattering in brain tissue, light-emitting implants are needed to bring patterned illumination to deep brain regions. A promising solution is silicon neural probes with integrated nanophotonic circuits that form tailored beam patterns without lenses. Here we propose neural probes with grating-based light emitters that generate a single steerable beam. The light emitters, optimized for blue or amber light, combine end-fire optical phased arrays with slab gratings to suppress higher-order sidelobes. In vivo experiments in mice demonstrated that the optical phased array provided sufficient power for optogenetic stimulation. While beam steering performance in tissue reveals challenges, including beam broadening from scattering and the need for a wider steering range, this proof-of-concept demonstration illustrates the design principles for realizing compact optical phased arrays capable of continuous single-beam scanning, laying the groundwork for advancing optical phased arrays toward targeted optogenetic stimulation.

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.

Implantable photonic neural probes with out-of-plane focusing grating emitters

We have designed, fabricated, and characterized implantable silicon neural probes with nanophotonic grating emitters that focus the emitted light at a specified distance above the surface of the probe for spatially precise optogenetic targeting of neurons. Using the holographic principle, we designed gratings for wavelengths of 488 and 594 nm, targeting the excitation spectra of the optogenetic actuators Channelrhodopsin-2 and Chrimson, respectively. The measured optical emission pattern of these emitters in non-scattering medium and tissue matched well with simulations. To our knowledge, this is the first report of focused spots with the size scale of a neuron soma in brain tissue formed from implantable neural probes.

Neurophotonics: a comprehensive review, current challenges and future trends

The human brain, with its vast network of billions of neurons and trillions of synapses (connections) between diverse cell types, remains one of the greatest mysteries in science and medicine. Despite extensive research, an understanding of the underlying mechanisms that drive normal behaviors and response to disease states is still limited. Advancement in the Neuroscience field and development of therapeutics for related pathologies requires innovative technologies that can provide a dynamic and systematic understanding of the interactions between neurons and neural circuits. In this work, we provide an up-to-date overview of the evolution of neurophotonic approaches in the last 10 years through a multi-source, literature analysis. From an initial corpus of 243 papers retrieved from Scopus, PubMed and WoS databases, we have followed the PRISMA approach to select 56 papers in the area. Following a full-text evaluation of these 56 scientific articles, six main areas of applied research were identified and discussed: (1) Advanced optogenetics, (2) Multimodal neural interfaces, (3) Innovative therapeutics, (4) Imaging devices and probes, (5) Remote operations, and (6) Microfluidic platforms. For each area, the main technologies selected are discussed according to the photonic principles applied, the neuroscience application evaluated and the more indicative results of efficiency and scientific potential. This detailed analysis is followed by an outlook of the main challenges tackled over the last 10 years in the Neurophotonics field, as well as the main technological advances regarding specificity, light delivery, multimodality, imaging, materials and system designs. We conclude with a discussion of considerable challenges for future innovation and translation in Neurophotonics, from light delivery within the brain to physical constraints and data management strategies.

Development of wafer-scale multifunctional nanophotonic neural probes for brain activity mapping

Optical techniques, such as optogenetic stimulation and functional fluorescence imaging, have been revolutionary for neuroscience by enabling neural circuit analysis with cell-type specificity. To probe deep brain regions, implantable light sources are crucial. Silicon photonics, commonly used for data communications, shows great promise in creating implantable devices with complex optical systems in a compact form factor compatible with high volume manufacturing practices. This article reviews recent developments of wafer-scale multifunctional nanophotonic neural probes. The probes can be realized on 200 or 300 mm wafers in commercial foundries and integrate light emitters for photostimulation, microelectrodes for electrophysiological recording, and microfluidic channels for chemical delivery and sampling. By integrating active optical devices to the probes, denser emitter arrays, enhanced on-chip biosensing, and increased ease of use may be realized. Silicon photonics technology makes possible highly versatile implantable neural probes that can transform neuroscience experiments.

Flexible neural probes: a review of the current advantages, drawbacks, and future demands

Brain diseases affect millions of people and have a huge social and economic impact. The use of neural probes for studies in animals has been the main approach to increasing knowledge about neural network functioning. Ultimately, neuroscientists are trying to develop new and more effective therapeutic approaches to treating neurological disorders. The implementation of neural probes with multifunctionalities (electrical, optical, and fluidic interactions) has been increasing in the last few years, leading to the creation of devices with high temporal and spatial resolution. Increasing the applicability of, and elements integrated into, neural probes has also led to the necessity to create flexible interfaces, reducing neural tissue damage during probe implantation and increasing the quality of neural acquisition data. In this paper, we review the fabrication, characterization, and validation of several types of flexible neural probes, exploring the main advantages and drawbacks of these devices. Finally, future developments and applications are covered. Overall, this review aims to present the currently available flexible devices and future appropriate avenues for development as possible guidance for future engineered devices.

Understanding the nervous system: lessons from Frontiers in Neurophotonics

The Frontiers in Neurophotonics Symposium is a biennial event that brings together neurobiologists and physicists/engineers who share interest in the development of leading-edge photonics-based approaches to understand and manipulate the nervous system, from its individual molecular components to complex networks in the intact brain. In this Community paper, we highlight several topics that have been featured at the symposium that took place in October 2022 in Québec City, Canada.

Implantable photonic neural probes with 3D-printed microfluidics and applications to uncaging

Advances in chip-scale photonic-electronic integration are enabling a new generation of foundry-manufacturable implantable silicon neural probes incorporating nanophotonic waveguides and microelectrodes for optogenetic stimulation and electrophysiological recording in neuroscience research. Further extending neural probe functionalities with integrated microfluidics is a direct approach to achieve neurochemical injection and sampling capabilities. In this work, we use two-photon polymerization 3D printing to integrate microfluidic channels onto photonic neural probes, which include silicon nitride nanophotonic waveguides and grating emitters. The customizability of 3D printing enables a unique geometry of microfluidics that conforms to the shape of each neural probe, enabling integration of microfluidics with a variety of existing neural probes while avoiding the complexities of monolithic microfluidics integration. We demonstrate the photonic and fluidic functionalities of the neural probes via fluorescein injection in agarose gel and photoloysis of caged fluorescein in solution and in fixed brain tissue.

Monolithically integrated, broadband, high-efficiency silicon nitride-on-silicon waveguide photodetectors in a visible-light integrated photonics platform

Visible and near-infrared spectrum photonic integrated circuits are quickly becoming a key technology to address the scaling challenges in quantum information and biosensing. Thus far, integrated photonic platforms in this spectral range have lacked integrated photodetectors. Here, we report silicon nitride-on-silicon waveguide photodetectors that are monolithically integrated in a visible light photonic platform on silicon. Owing to a leaky-wave silicon nitride-on-silicon design, the devices achieved a high external quantum efficiency of >60% across a record wavelength span from λ ~ 400 nm to ~640 nm, an opto-electronic bandwidth up to 9 GHz, and an avalanche gain-bandwidth product up to 173 ± 30 GHz. As an example, a photodetector was integrated with a wavelength-tunable microring in a single chip for on-chip power monitoring.

Real-Time In Vivo Sensing of Nitric Oxide Using Photonic Microring Resonators

Real-time in vivo detection of biomarkers, particularly nitric oxide (NO), is of utmost importance for critical healthcare monitoring, therapeutic dosing, and fundamental understanding of NO's role in regulating many physiological processes. However, detection of NO in a biological medium is challenging due to its short lifetime and low concentration. Here, we demonstrate for the first time that photonic microring resonators (MRRs) can provide real-time, direct, and in vivo detection of NO in a mouse wound model. The MRR encodes the NO concentration information into its transfer function in the form of a resonance wavelength shift. We show that these functionalized MRRs, fabricated using complementary metal oxide semiconductor (CMOS) compatible processes, can achieve sensitive detection of NO (sub-μM) with excellent specificity and no apparent performance degradation for more than 24 h of operation in biological medium. With alternative functionalizations, this compact lab-on-chip optical sensing platform could support real-time in vivo detection of myriad of biochemical species.

Cleanroom strategies for micro- and nano-fabricating flexible implantable neural electronics

Implantable electronic neural interfaces typically take the form of probes and are made with rigid materials such as silicon and metals. These have advantages such as compatibility with integrated microchips, simple implantation and high-density nanofabrication but tend to be lacking in terms of biointegration, biocompatibility and durability due to their mechanical rigidity. This leads to damage to the device or, more importantly, the brain tissue surrounding the implant. Flexible polymer-based probes offer superior biocompatibility in terms of surface biochemistry and better matched mechanical properties. Research which aims to bring the fabrication of electronics on flexible polymer substrates to the nano-regime is remarkably sparse, despite the push for flexible consumer electronics in the last decade or so. Cleanroom-based nanofabrication techniques such as photolithography have been used as pattern transfer methods by the semiconductor industry to produce single nanometre scale devices and are now also used for making flexible circuit boards. There is still much scope for miniaturizing flexible electronics further using photolithography, bringing the possibility of nanoscale, non-invasive, high-density flexible neural interfacing. This work explores the fabrication challenges of using photolithography and complementary techniques in a cleanroom for producing flexible electronic neural probes with nanometre-scale features. This article is part of the theme issue 'Advanced neurotechnologies: translating innovation for health and well-being'.

Toward an integrative neurovascular framework for studying brain networks

Brain functional connectivity based on the measure of blood oxygen level-dependent (BOLD) functional magnetic resonance imaging (fMRI) signals has become one of the most widely used measurements in human neuroimaging. However, the nature of the functional networks revealed by BOLD fMRI can be ambiguous, as highlighted by a recent series of experiments that have suggested that typical resting-state networks can be replicated from purely vascular or physiologically driven BOLD signals. After going through a brief review of the key concepts of brain network analysis, we explore how the vascular and neuronal systems interact to give rise to the brain functional networks measured with BOLD fMRI. This leads us to emphasize a view of the vascular network not only as a confounding element in fMRI but also as a functionally relevant system that is entangled with the neuronal network. To study the vascular and neuronal underpinnings of BOLD functional connectivity, we consider a combination of methodological avenues based on multiscale and multimodal optical imaging in mice, used in combination with computational models that allow the integration of vascular information to explain functional connectivity.

Free-Space Applications of Silicon Photonics: A Review

Silicon photonics has recently expanded its applications to delivering free-space emissions for detecting or manipulating external objects. The most notable example is the silicon optical phased array, which can steer a free-space beam to achieve a chip-scale solid-state LiDAR. Other examples include free-space optical communication, quantum photonics, imaging systems, and optogenetic probes. In contrast to the conventional optical system consisting of bulk optics, silicon photonics miniaturizes an optical system into a photonic chip with many functional waveguiding components. By leveraging the mature and monolithic CMOS process, silicon photonics enables high-volume production, scalability, reconfigurability, and parallelism. In this paper, we review the recent advances in beam steering technologies based on silicon photonics, including optical phased arrays, focal plane arrays, and dispersive grating diffraction. Various beam-shaping technologies for generating collimated, focused, Bessel, and vortex beams are also discussed. We conclude with an outlook of the promises and challenges for the free-space applications of silicon photonics.

Development of nano- and microdevices for the next generation of biotechnology, wearables and miniaturized instrumentation

This is a short communication based on recent high-impact publications related to how various chemical materials and substrate modifications could be tuned for nano- and microdevices, where their application for high point-of-care bioanalysis and further applications in life science is discussed. Hence, they have allowed different high-impact research topics in a variety of fields, from the control of nanoscale to functional microarchitectures embedded in various support materials to obtain a device for a given application or use. Thus, their incorporation in standard instrumentation is shown, as well as in new optical setups to record different classical and non-classical light, signaling, and energy modes at a variety of wavelengths and energy levels. Moreover, the development of miniaturized instrumentation was also contemplated. In order to develop these different levels of technology, the chemistry, physics and engineering of materials were discussed. In this manner, a number of subjects that allowed the design and manufacture of devices could be found. The following could be mentioned by way of example: (i) nanophotonics; (ii) design, synthesis and tuning of advanced nanomaterials; (iii) classical and non-classical light generation within the near field; (iv) microfluidics and nanofluidics; (v) signal waveguiding; (vi) quantum-, nano- and microcircuits; (vii) materials for nano- and microplatforms, and support substrates and their respective modifications for targeted functionalities. Moreover, nano-optics in in-flow devices and chips for biosensing were discussed, and perspectives on biosensing and single molecule detection (SMD) applications. In this perspective, new insights about precision nanomedicine based on genomics and drug delivery systems were obtained, incorporating new advanced diagnosis methods based on lab-on-particles, labs-on-a-chip, gene therapies, implantable devices, portable miniaturized instrumentation, single molecule detection for biophotonics, and neurophotonics. In this manner, this communication intends to highlight recent reports and developments of nano- and microdevices and further approaches towards the incorporation of developments in nanophotonics and biophotonics in the design of new materials based on different strategies and enhanced techniques and methods. Recent proofs of concept are discussed that could allow new substrates for device manufacturing. Thus, physical phenomena and materials chemistry with accurate control within the nanoscale were introduced into the discussion. In this manner, new potential sources of ideas and strategies for the next generation of technology in many research and development fields are showcased.

Optical phased array neural probes for beam-steering in brain tissue

Implantable silicon neural probes with integrated nanophotonic waveguides can deliver patterned dynamic illumination into brain tissue at depth. Here, we introduce neural probes with integrated optical phased arrays and demonstrate optical beam steering in vitro. Beam formation in brain tissue is simulated and characterized. The probes are used for optogenetic stimulation and calcium imaging.

Power-efficient silicon nitride thermo-optic phase shifters for visible light

We demonstrate power-efficient, thermo-optic, silicon nitride waveguide phase shifters for blue, green, and yellow wavelengths. The phase shifters operated with low power consumption due to a suspended structure and multi-pass waveguide design. The devices were fabricated on 200-mm silicon wafers using deep ultraviolet lithography as part of an active visible-light integrated photonics platform. The measured power consumption to achieve a π phase shift (averaged over multiple devices) was 0.78, 0.93, 1.09, and 1.20 mW at wavelengths of 445, 488, 532, and 561 nm, respectively. The phase shifters were integrated into Mach-Zehnder interferometer switches, and 10 - 90% rise(fall) times of about 570(590) μs were measured.

Multicore fibers with 10 and 16 single-mode cores for the visible spectrum

We report multicore fibers (MCFs) with 10 and 16 linearly distributed cores with single-mode operation in the visible spectrum. The average propagation loss of the cores is 0.06 dB/m at λ = 445 nm and < 0.03 dB/m at wavelengths longer than 488 nm. The low inter-core crosstalk and nearly identical performance of the cores make these MCFs suitable for spatial division multiplexing in the visible spectrum. As a proof-of-concept application, one of the MCFs was coupled to an implantable neural probe to spatially address light-emitting gratings on the probe.

Low-loss broadband bi-layer edge couplers for visible light

Low-loss broadband fiber-to-chip coupling is currently challenging for visible-light photonic-integrated circuits (PICs) that need both high confinement waveguides for high-density integration and a minimum feature size above foundry lithographical limit. Here, we demonstrate bi-layer silicon nitride (SiN) edge couplers that have ≤ 4 dB/facet coupling loss with the Nufern S405-XP fiber over a broad optical wavelength range from 445 to 640 nm. The design uses a thin layer of SiN to expand the mode at the facet and adiabatically transfers the input light into a high-confinement single-mode waveguide (150-nm thick) for routing, while keeping the minimum nominal lithographic feature size at 150 nm. The achieved fiber-to-chip coupling loss is about 3 to 5 dB lower than that of single-layer designs with the same waveguide confinement and minimum feature size limitation.