MAPSYNE: Miniaturized micropipette system combined with high-density microelectrode arrays for automated manipulation of neuronal networks in-vitro.

We present MAPSYNE, a miniaturized and automated system combining a high-density microelectrode array (HD-MEA) and a movable micropipette for studying, monitoring, and perturbing neurons in vitro. The system involves an all-electrical approach to automatically move a glass micropipette towards a target location on the HD-MEA surface, without the need for a microscope. Two methods of performing blind navigation are employed, (i) stop-measure-go approach wherein the pipette moves for a predefined distance before measuring its location then the process is repeated until the pipette reaches its destination, and (ii) predictive approach wherein the pipette is continuously tracked and moved. This automated system can be applied for unsupervised single-cell manipulation of neurons in a network, such as electroporation and local delivery of compounds.

Author Correction: Accurate signal-source localization in brain slices by means of high-density microelectrode arrays.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Versatile live-cell activity analysis platform for characterization of neuronal dynamics at single-cell and network level.

Chronic imaging of neuronal networks in vitro has provided fundamental insights into mechanisms underlying neuronal function. Current labeling and optical imaging methods, however, cannot be used for continuous and long-term recordings of the dynamics and evolution of neuronal networks, as fluorescent indicators can cause phototoxicity. Here, we introduce a versatile platform for label-free, comprehensive and detailed electrophysiological live-cell imaging of various neurogenic cells and tissues over extended time scales. We report on a dual-mode high-density microelectrode array, which can simultaneously record in (i) full-frame mode with 19,584 recording sites and (ii) high-signal-to-noise mode with 246 channels. We set out to demonstrate the capabilities of this platform with recordings from primary and iPSC-derived neuronal cultures and tissue preparations over several weeks, providing detailed morpho-electrical phenotypic parameters at subcellular, cellular and network level. Moreover, we develop reliable analysis tools, which drastically increase the throughput to infer axonal morphology and conduction speed.

Large-Scale, High-Resolution Microelectrode Arrays for Interrogation of Neurons and Networks.

High-density microelectrode arrays (HD-MEAs) are increasingly being used for the observation and manipulation of neurons and networks in vitro. Large-scale electrode arrays allow for long-term extracellular recording of the electrical activity from thousands of neurons simultaneously. Beyond population activity, it has also become possible to extract information of single neurons at subcellular level (e.g., the propagation of action potentials along axons). In effect, HD-MEAs have become an electrical imaging platform for label-free extraction of the structure and activation of cells in cultures and tissues. The quality of HD-MEA data depends on the resolution of the electrode array and the signal-to-noise ratio. In this chapter, we begin with an introduction to HD-MEA signals. We provide an overview of the developments on complementary metal-oxide-semiconductor or CMOS-based HD-MEA technology. We also discuss the factors affecting the performance of HD-MEAs and the trending application requirements that drive the efforts for future devices. We conclude with an outlook on the potential of HD-MEAs for advancing basic neuroscience and drug discovery.

Accurate signal-source localization in brain slices by means of high-density microelectrode arrays.

Extracellular recordings by means of high-density microelectrode arrays (HD-MEAs) have become a powerful tool to resolve subcellular details of single neurons in active networks grown from dissociated cells. To extend the application of this technology to slice preparations, we developed models describing how extracellular signals, produced by neuronal cells in slices, are detected by microelectrode arrays. The models help to analyze and understand the electrical-potential landscape in an in vitro HD-MEA-recording scenario based on point-current sources. We employed two modeling schemes, (i) a simple analytical approach, based on the method of images (MoI), and (ii) an approach, based on finite-element methods (FEM). We compared and validated the models with large-scale, high-spatiotemporal-resolution recordings of slice preparations by means of HD-MEAs. We then developed a model-based localization algorithm and compared the performance of MoI and FEM models. Both models provided accurate localization results and a comparable and negligible systematic error, when the point source was in saline, a condition similar to cell-culture experiments. Moreover, the relative random error in the x-y-z-localization amounted only up to 4.3% for z-distances up to 200 µm from the HD-MEA surface. In tissue, the systematic errors of both, MoI and FEM models were significantly higher, and a pre-calibration was required. Nevertheless, the FEM values proved to be closer to the tissue experimental results, yielding 5.2 µm systematic mean error, compared to 22.0 µm obtained with MoI. These results suggest that the medium volume or "saline height", the brain slice thickness and anisotropy, and the location of the reference electrode, which were included in the FEM model, considerably affect the extracellular signal and localization performance, when the signal source is at larger distance to the array. After pre-calibration, the relative random error of the z-localization in tissue was only 3% for z-distances up to 200 µm. We then applied the model and related detailed understanding of extracellular recordings to achieve an electrically-guided navigation of a stimulating micropipette, solely based on the measured HD-MEA signals, and managed to target spontaneously active neurons in an acute brain slice for electroporation.

Technologies to Study Action Potential Propagation With a Focus on HD-MEAs.

Axons convey information in neuronal circuits via reliable conduction of action potentials (APs) from the axon initial segment (AIS) to the presynaptic terminals. Recent experimental findings increasingly evidence that the axonal function is not limited to the simple transmission of APs. Advances in subcellular-resolution recording techniques have shown that axons display activity-dependent modulation in spike shape and conduction velocity, which influence synaptic strength and latency. We briefly review here, how recent methodological developments facilitate the understanding of the axon physiology. We included the three most common methods, i.e., genetically encoded voltage imaging (GEVI), subcellular patch-clamp and high-density microelectrode arrays (HD-MEAs). We then describe the potential of using HD-MEAs in studying axonal physiology in more detail. Due to their robustness, amenability to high-throughput and high spatiotemporal resolution, HD-MEAs can provide a direct functional electrical readout of single cells and cellular ensembles at subcellular resolution. HD-MEAs can, therefore, be employed in investigating axonal pathologies, the effects of large-scale genomic interventions (e.g., with RNAi or CRISPR) or in compound screenings. A combination of extracellular microelectrode arrays (MEAs), intracellular microelectrodes and optical imaging may potentially reveal yet unexplored repertoires of axonal functions.

Dual-mode Microelectrode Array Featuring 20k Electrodes and High SNR for Extracellular Recording of Neural Networks.

In recent electrophysiological studies, CMOS-based high-density microelectrode arrays (HD-MEA) have been widely used for studies of both in-vitro and in-vivo neuronal signals and network behavior. Yet, an open issue in MEA design concerns the tradeoff between signal-to-noise ratio (SNR) and number of readout channels. Here we present a new HD-MEA design in 0.18 µm CMOS technology, consisting of 19,584 electrodes at a pitch of 18.0 µm. By combing two readout structures, namely active-pixel-sensor (APS) and switch-matrix (SM) on a single chip, the dual-mode HD-MEA is capable of recording simultaneously from the entire array and achieving high signal-to-noise-ratio recordings on a subset of electrodes. The APS readout circuits feature a noise level of 10.9 µVrms for the action potential band (300 Hz - 5 kHz), while the noise level for the switch-matrix readout is 3.1 µVrms.

Optimal Electrode Size for Multi-Scale Extracellular-Potential Recording From Neuronal Assemblies.

Advances in microfabrication technology have enabled the production of devices containing arrays of thousands of closely spaced recording electrodes, which afford subcellular resolution of electrical signals in neurons and neuronal networks. Rationalizing the electrode size and configuration in such arrays demands consideration of application-specific requirements and inherent features of the electrodes. Tradeoffs among size, spatial density, sensitivity, noise, attenuation, and other factors are inevitable. Although recording extracellular signals from neurons with planar metal electrodes is fairly well established, the effects of the electrode characteristics on the quality and utility of recorded signals, especially for small, densely packed electrodes, have yet to be fully characterized. Here, we present a combined experimental and computational approach to elucidating how electrode size, and size-dependent parameters, such as impedance, baseline noise, and transmission characteristics, influence recorded neuronal signals. Using arrays containing platinum electrodes of different sizes, we experimentally evaluated the electrode performance in the recording of local field potentials (LFPs) and extracellular action potentials (EAPs) from the following cell preparations: acute brain slices, dissociated cell cultures, and organotypic slice cultures. Moreover, we simulated the potential spatial decay of point-current sources to investigate signal averaging using known signal sources. We demonstrated that the noise and signal attenuation depend more on the electrode impedance than on electrode size, per se, especially for electrodes <10 µm in width or diameter to achieve high-spatial-resolution readout. By minimizing electrode impedance of small electrodes (<10 µm) via surface modification, we could maximize the signal-to-noise ratio to electrically visualize the propagation of axonal EAPs and to isolate single-unit spikes. Due to the large amplitude of LFP signals, recording quality was high and nearly independent of electrode size. These findings should be of value in configuring in vitro and in vivo microelectrode arrays for extracellular recordings with high spatial resolution in various applications.

The Axon Initial Segment is the Dominant Contributor to the Neuron's Extracellular Electrical Potential Landscape.

Extracellular voltage fields, produced by a neuron's action potentials, provide a widely used means for studying neuronal and neuronal-network function. The neuron's soma and dendrites are thought to drive the extracellular action potential (EAP) landscape, while the axon's contribution is usually considered less important. However, by recording voltages of single neurons in dissociated rat cortical cultures and Purkinje cells in acute mouse cerebellar slices through hundreds of densely packed electrodes, it is found, instead, that the axon initial segment dominates the measured EAP landscape, and, surprisingly, the soma only contributes to a minor extent. As expected, the recorded dominant signal has negative polarity (charge entering the cell) and initiates at the distal end. Interestingly, signals with positive polarity (charge exiting the cell) occur near some but not all dendritic branches and occur after a delay. Such basic knowledge about which neuronal compartments contribute to the extracellular voltage landscape is important for interpreting results from all electrical readout schemes. Finally, initiation of the electrical activity at the distal end of the axon initial segment (AIS) and subsequent spreading into the axon proper and backward through the proximal AIS toward the soma are confirmed. The corresponding extracellular waveforms across different neuronal compartments could be tracked.

Impedance Spectroscopy and Electrophysiological Imaging of Cells With a High-Density CMOS Microelectrode Array System.

A monolithic multi-functional CMOS microelectrode array system was developed that enables label-free electrochemical impedance spectroscopy of cells in vitro at high spatiotemporal resolution. The electrode array includes 59,760 platinum microelectrodes, densely packed within a 4.5 mm × 2.5 mm sensing region at a pitch of 13.5 µm. A total of 32 on-chip lock-in amplifiers can be used to measure the impedance of any arbitrarily chosen subset of electrodes in the array. A sinusoidal voltage, generated by an on-chip waveform generator with a frequency range from 1 Hz to 1 MHz, was applied to the reference electrode. The sensing currents through the selected recording electrodes were amplified, demodulated, filtered, and digitized to obtain the magnitude and phase information of the respective impedances. The circuitry consumes only 412 µW at 3.3 V supply voltage and occupies only 0.1 mm2, for each channel. The system also included 2048 extracellular action-potential recording channels on the same chip. Proof of concept measurements of electrical impedance imaging and electrophysiology recording of cardiac cells and brain slices are demonstrated in this paper. Optical and impedance images showed a strong correlation.

Multiple Single-Unit Long-Term Tracking on Organotypic Hippocampal Slices Using High-Density Microelectrode Arrays.

A novel system to cultivate and record from organotypic brain slices directly on high-density microelectrode arrays (HD-MEA) was developed. This system allows for continuous recording of electrical activity of specific individual neurons at high spatial resolution while monitoring at the same time, neuronal network activity. For the first time, the electrical activity patterns of single neurons and the corresponding neuronal network in an organotypic hippocampal slice culture were studied during several consecutive weeks at daily intervals. An unsupervised iterative spike-sorting algorithm, based on PCA and k-means clustering, was developed to assign the activities to the single units. Spike-triggered average extracellular waveforms of an action potential recorded across neighboring electrodes, termed "footprints" of single-units were generated and tracked over weeks. The developed system offers the potential to study chronic impacts of drugs or genetic modifications on individual neurons in slice preparations over extended times.

Automated navigation of a glass micropipette on a high-density microelectrode array.

High-density microelectrode arrays (HDMEAs) provide the capability to monitor the extracellular electric potential of multiple neurons at subcellular resolution over extended periods of time. In contrast, patch clamp allows for intracellular, sub-threshold recordings from a single patched neuron for very limited time on the order of an hour. Therefore, it will be beneficial to combine HDMEA and patch clamp for simultaneous intra- and extracellular recording of neuronal activity. Previously, it has been shown that the HDMEA can be used to localize and steer a glass micropipette towards a target location without using an optical microscope [1]. Here, we present an automated system, implemented in LabVIEW, which automatically locates and moves the glass micropipette towards a user-defined target. The presented system constitutes a first step towards developing an automated system to navigate a pipette to patch a neuron in vitro.

Revealing neuronal function through microelectrode array recordings.

Microelectrode arrays and microprobes have been widely utilized to measure neuronal activity, both in vitro and in vivo. The key advantage is the capability to record and stimulate neurons at multiple sites simultaneously. However, unlike the single-cell or single-channel resolution of intracellular recording, microelectrodes detect signals from all possible sources around every sensor. Here, we review the current understanding of microelectrode signals and the techniques for analyzing them. We introduce the ongoing advancements in microelectrode technology, with focus on achieving higher resolution and quality of recordings by means of monolithic integration with on-chip circuitry. We show how recent advanced microelectrode array measurement methods facilitate the understanding of single neurons as well as network function.