Name: using neuron spiking activity to trigger closed-loop stimuli in neurophysiological experiments
Uploaded: 2019-11-12T11:00:00
Description: Watch this Scientific Journal Video about Using Neuron Spiking Activity to Trigger Closed-Loop Stimuli in Neurophysiological Experiments at JoVE.com

This work was supported by NSERC Discovery grants to AL and AG.

All procedures described here were performed under an Animal Research Protocol approved by the University of Lethbridge Animal Welfare Committee.
1. Surgery
NOTE: The surgery procedures used to implant probes for neurophysiological recordings have been presented in other publications24,25,26. The exact details of the surgery for closed-loop stimulation depend on the type of r...

<ol>
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The protocol described here, shows how to use a standard neurophysiological recording system to perform closed-loop stimulation. This protocol allows neuroscientists with limited expertise in computer science to rapidly implement a variety of closed-loop experiments with little cost. Such experiments are often necessary to study causal interactions in the brain.
After preparing an animal and installing the software (Steps 1 &amp; 2), the closed-loop experiment consists of two separate stages. ...

The goal of this protocol is to demonstrate how to implement closed-loop stimulation in neurophysiological experiments. The typical setup for closed-loop experiments in neuroscience involves triggering stimuli based on the online readout of neuronal activity. This, in turn, causes modifications in the brain activity, thus closing the feedback loop1,2. Such closed-loop experiments provide multiple benefits over standard open-loop setups, especially when combined with optogenetics, which allows researchers to target a specific subset of neurons. For example, Siegle and Wilson used closed-loop manipulations to study the role of theta oscillations in information processing3. They demonstrated that stimulating hippocampal neurons on the falling phase of theta oscillations had different effects on behavior than applying the same stimulation on the rising phase. Closed-loop experiments are also becoming increasingly important in preclinical studies. For instance, multiple epilepsy studies have shown that neuronal stimulation triggered on seizure onset is an effective approach to reduce the severity of seizures4,5,6. Moreover, systems for automated seizure detection and the contingent delivery of therapy7,8 showed significant benefits in epilepsy patients9,10,11,12. Another application area with rapid advancement of closed-loop methodologies is the control of neuroprosthetics with cortical brain&#8211;machine interfaces. This is because providing instantaneous feedback to users of prosthetic devices significantly improves accuracy and capability13.
In recent years, several labs have developed custom systems for the simultaneous electrical recording of neuronal activity and delivery of stimuli in a closed-loop system14,15,16,17,18. Although many of those setups have impressive characteristics, it is not always easy to implement them in other labs. This is because the systems often demand experienced technicians to assemble the required electronics and other necessary hardware and software components.
Therefore, in order to facilitate the adoption of closed-loop experiments in neuroscience research, this paper provides a protocol and Matlab code to convert an open-loop electrophysiological recording setup19,20,21,22 into a closed-loop system2,6,23. This protocol is designed to work with the Digital Lynx recording hardware, a popular laboratory system for neuronal population recordings. A typical experiment consists of the following: 1) Recording 5-20 minutes of spiking data; 2) Spike sorting to create neuronal templates; 3) Using these templates to perform online detection of neural activity patterns; and 4) Triggering stimulation or experimental events when user-specified patterns are detected.

<table>
	<tbody>
		<tr>
			<td>Baytril</td>
			<td>Bayer, Mississauga, CA</td>
			<td>DIN 02169428</td>
			<td>antibiotic; 50 mg/mL</td>
		</tr>
		<tr>
			<td>Cheetah 6.4</td>
			<td>NeuraLynx, Tucson, AZ</td>
			<td>6.4.0.beta</td>
			<td>Software interfaces for data acquisition&#160;</td>
		</tr>
		<tr>
			<td>Digital Lynx 4SX</td>
			<td>NeuraLynx, Tucson, AZ</td>
			<td>4SX</td>
			<td>recording equipment</td>
		</tr>
		<tr>
			<td>Headstage transmitter</td>
			<td>TBSI</td>
			<td>B10-3163-GK</td>
			<td>transmits the neural signal to the receiver</td>
		</tr>
		<tr>
			<td>Isoflurane</td>
			<td>Fresenius Kabi, Toronto, CA</td>
			<td>DIN 02237518</td>
			<td>inhalation anesthetic</td>
		</tr>
		<tr>
			<td>Jet Denture Powder &#38; Liqud</td>
			<td>Lang Dental, Wheeling, US</td>
			<td>1230</td>
			<td>dental acrylic</td>
		</tr>
		<tr>
			<td>Lacri-Lube</td>
			<td>Allergan, Markham, CA</td>
			<td>DIN 00210889</td>
			<td>eye ointment</td>
		</tr>
		<tr>
			<td>Lido-2</td>
			<td>Rafter 8, Calgary</td>
			<td>DIN 00654639</td>
			<td>local anesthetic; 20 mg/mL</td>
		</tr>
		<tr>
			<td>Matlab</td>
			<td>Mathworks</td>
			<td>R2018b</td>
			<td>software for signal processing and triggering external events</td>
		</tr>
		<tr>
			<td>Metacam</td>
			<td>Boehringer, Ingelheim, DE</td>
			<td>DIN 02240463</td>
			<td>analgesic; 5 mg/mL</td>
		</tr>
		<tr>
			<td>Netcom</td>
			<td>NeuraLynx</td>
			<td>v1</td>
			<td>Application Programming Interface (API) that communicates with Cheetah</td>
		</tr>
		<tr>
			<td>Silicone probe</td>
			<td>Cambridge Neurotech</td>
			<td>ASSY-156-DBC2</td>
			<td>implanted device</td>
		</tr>
		<tr>
			<td>SpikeSort 3D&#160;</td>
			<td>NeuraLynx, Tucson, AZ</td>
			<td>SS3D</td>
			<td>spike waveform-to-cell classification tools</td>
		</tr>
		<tr>
			<td>Wireless Radio Receiver</td>
			<td>TBSI</td>
			<td>911-1062-00</td>
			<td>transmits the neural signal to the Digital Lynx</td>
		</tr>
	</tbody>
</table>

using neuron spiking activity to trigger closed-loop stimuli in neurophysiological experiments

Closed-loop neurophysiological systems use patterns of neuronal activity to trigger stimuli, which in turn affect brain activity. Such closed-loop systems are already found in clinical applications, and are important tools for basic brain research. A particularly interesting recent development is the integration of closed-loop approaches with optogenetics, such that specific patterns of neuronal activity can trigger optical stimulation of selected neuronal groups. However, setting up an electrophysiological system for closed-loop experiments can be difficult. Here, a ready-to-apply Matlab code is provided for triggering stimuli based on the activity of single or multiple neurons. This sample code can be easily modified based on individual needs. For instance, it shows how to trigger sound stimuli and how to change it to trigger an external device connected to a PC serial port. The presented protocol is designed to work with a popular neuronal recording system for animal studies (Neuralynx). The implementation of closed-loop stimulation is demonstrated in an awake rat.

Fisher-Brown Norway rats born and raised on-site were habituated to handling for two weeks prior to the experiment. A recording drive was surgically implanted, similar to methods described previously28,29,30,31,32,33,34. The neuronal signals were recorded at 32 kHz with a digital acquisition...

Watch this Scientific Journal Video about Using Neuron Spiking Activity to Trigger Closed-Loop Stimuli in Neurophysiological Experiments at JoVE.com

Using Neuron Spiking Activity to Trigger Closed-Loop Stimuli in Neurophysiological Experiments

This protocol demonstrates how to use an electrophysiological system for closed-loop stimulation triggered by neuronal activity patterns. Sample Matlab code that can be easily modified for different stimulation devices is also provided.

Closed-loop neurophysiological systems use patterns of neuronal activity to trigger stimuli, which in turn affect brain activity. Such closed-loop systems ...

This standard neurophysiological recording system can be used to perform a closed-loop stimulation which is useful for studying causal interactions in the brain. This protocol allows neuroscientists with only limited expertise in computer science to rapidly implement a variety of closed-loop experiments with little cost. Closed-loop experiments have becaming increasingly important for basic science and research.For instance, multiple epilepsy studies have shown that neuron stimulation trigger on seizure onset is an an effective approach to reduce the severity of seizures. To facilitate the adoption of closed-loop experiments in neuroscience research, this protocol provides MATLAB code to convert an open-loop electrophysiological recording system into a closed-loop system. This implementation of closed-loop stimulation is demonstrated in an awake rat.To install the Cheetah 6.4 Data Acquisition System, open the webpage for the software which includes libraries to interact with the Cheetah acquisitions system, and install SpikeSort-3D. Install the NetCom Development Package. Login to a MATLAB account to select the correct license, version, and operating system.Then, download the library for online event triggering as indicated and extract the files to the documents MATLAB folder. For data acquisition, open the Cheetah software and record spiking data to populate the template waveforms. After a few minutes, stop the data acquisition and perform a SpikeSort on the recorded data.Next, open SpikeSort3-D and click file menu and load spike file To select a spike file from the folder with the recorded data. Then, click cluster menu, autocluster using KlustaKwik, and run. To perform a closed-loop experiment, resume the data acquisition in Cheetah, and open MATLAB.Open ClosedLoop. M and click run. Alternatively, execute closed-loop in the command window.Browse to the recording folder and select one of the spiking data files to load the spike information defined in the initial recording. Click the appropriate check boxes under the plotted waveforms to select one or multiple neurons that will trigger stimulation. Define the minimum number of neurons that will trigger stimulation by entering an integer in the min matches text box and define the time window in which the spikes matching the different waveforms are considered coactive by entering a number into the window text box.Then, click send to begin the online triggering of events based on the spiking activity of the selected neurons. In this representative experiment, the rat was rested on a flower pot which was a familiar resting place during breaks in the behavioral experiments. Here, a representative simultaneous running of the recording software and the MATLAB program which displays spike waveforms acquired in real time can be observed.When spikes from predefined triggering clusters are detected, the waveforms are displayed with a bold dash line in the MATLAB figure window triggering a tone and providing a closed-loop system. In this figure, a representative histogram illustrating the delays between the time of generating an artificial spike and the time of inducing a triggered signal are shown. After preparing an animal, and installing the software, the closed-loop experiment consists of two main stages, the initial data acquisition and the closed-loop stimulation during which spikes trigger external stimuli.This protocol also allows the treating of a stimuli based on the activity of multiple neurons which is important for addressing questions about information processing in the brain. The advantages of this MATLAB solution are its low cost and flexibility in defining the activity patterns to trigger stimuli which can help in investigating a variety of neuroscientific questions.

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Research

JoVE Journal

Neuroscience

An Experimental Platform to Study the Closed-loop Performance of Brain-machine Interfaces

The non-stationary nature and variability of neuronal signals is a fundamental problem in brain-machine interfacing. We developed a brain-machine interface to assess the robustness of different control-laws applied to a closed-loop image stabilization task. Taking advantage of the well-characterized fly visuomotor pathway we record the electrical activity from an identified, motion-sensitive neuron, H1, to control the yaw rotation of a two-wheeled robot. The robot is equipped with 2 high-speed video cameras providing visual motion input to a fly placed in front of 2 CRT computer monitors. The activity of the H1 neuron indicates the direction and relative speed of the robot's rotation. The neural activity is filtered and fed back into the steering system of the robot by means of proportional and proportional/adaptive control. Our goal is to test and optimize the performance of various control laws under closed-loop conditions for a broader application also in other brain machine interfaces.

We use a closed-loop fly-machine interface to investigate general principles in neuronal control.

The non-stationary nature and variability of neuronal signals is a fundamental problem in brain-machine interfacing. We developed a brain-machine ...

The Neuromuscular Junction: Measuring Synapse Size, Fragmentation and Changes in Synaptic Protein Density Using Confocal Fluorescence Microscopy

The neuromuscular junction (NMJ) is the large, cholinergic relay synapse through which mammalian motor neurons control voluntary muscle contraction. Structural changes at the NMJ can result in neurotransmission failure, resulting in weakness, atrophy and even death of the muscle fiber. Many studies have investigated how genetic modifications or disease can alter the structure of the mouse NMJ. Unfortunately, it can be difficult to directly compare findings from these studies because they often employed different parameters and analytical methods. Three protocols are described here. The first uses maximum intensity projection confocal images to measure the area of acetylcholine receptor (AChR)-rich postsynaptic membrane domains at the endplate and the area of synaptic vesicle staining in the overlying presynaptic nerve terminal. The second protocol compares the relative intensities of immunostaining for synaptic proteins in the postsynaptic membrane. The third protocol uses Fluorescence Resonance Energy Transfer (FRET) to detect changes in the packing of postsynaptic AChRs at the endplate. The protocols have been developed and refined over a series of studies. Factors that influence the quality and consistency of results are discussed and normative data are provided for NMJs in healthy young adult mice.

The neuromuscular junction (NMJ) is altered in a variety of conditions that can sometimes culminate in synaptic failure. This report describes fluorescence microscope-based methods to quantify such structural changes.

The neuromuscular junction (NMJ) is the large, cholinergic relay synapse through which mammalian motor neurons control voluntary muscle contraction. ...

Real-time Electrophysiology: Using Closed-loop Protocols to Probe Neuronal Dynamics and Beyond

Experimental neuroscience is witnessing an increased interest in the development and application of novel and often complex, closed-loop protocols, where the stimulus applied depends in real-time on the response of the system. Recent applications range from the implementation of virtual reality systems for studying motor responses both in mice1 and in zebrafish2, to control of seizures following cortical stroke using optogenetics3. A key advantage of closed-loop techniques resides in the capability of probing higher dimensional properties that are not directly accessible or that depend on multiple variables, such as neuronal excitability4 and reliability, while at the same time maximizing the experimental throughput. In this contribution and in the context of cellular electrophysiology, we describe how to apply a variety of closed-loop protocols to the study of the response properties of pyramidal cortical neurons, recorded intracellularly with the patch clamp technique in acute brain slices from the somatosensory cortex of juvenile rats. As no commercially available or open source software provides all the features required for efficiently performing the experiments described here, a new software toolbox called LCG5 was developed, whose modular structure maximizes reuse of computer code and facilitates the implementation of novel experimental paradigms. Stimulation waveforms are specified using a compact meta-description and full experimental protocols are described in text-based configuration files. Additionally, LCG has a command-line interface that is suited for repetition of trials and automation of experimental protocols.

Closed-loop protocols are becoming increasingly widespread in modern day electrophysiology. We present a simple, versatile and inexpensive way to perform complex electrophysiological protocols in cortical pyramidal neurons in vitro, using a desktop computer and a digital acquisition board.

Experimental neuroscience is witnessing an increased interest in the development and application of novel and often complex, closed-loop protocols, where ...

Closed-loop Neuro-robotic Experiments to Test Computational Properties of Neuronal Networks

Information coding in the Central Nervous System (CNS) remains unexplored. There is mounting evidence that, even at a very low level, the representation of a given stimulus might be dependent on context and history. If this is actually the case, bi-directional interactions between the brain (or if need be a reduced model of it) and sensory-motor system can shed a light on how encoding and decoding of information is performed. Here an experimental system is introduced and described in which the activity of a neuronal element (i.e., a network of neurons extracted from embryonic mammalian hippocampi) is given context and used to control the movement of an artificial agent, while environmental information is fed back to the culture as a sequence of electrical stimuli. This architecture allows a quick selection of diverse encoding, decoding, and learning algorithms to test different hypotheses on the computational properties of neuronal networks.

In this paper, an experimental framework to perform closed-loop experiments is presented, in which information processing (i.e., coding and decoding) and learning of neuronal assemblies are studied during the continuous interaction with a robotic body.

Information coding in the Central Nervous System (CNS) remains unexplored. There is mounting evidence that, even at a very low level, the representation ...

Immunohistochemical Visualization of Hippocampal Neuron Activity After Spatial Learning in a Mouse Model of Neurodevelopmental Disorders

Induction of phosphorylated extracellular-regulated kinase (pERK) is a reliable molecular readout of learning-dependent neuronal activation. Here, we describe a pERK immunohistochemistry protocol to study the profile of hippocampal neuron activation following exposure to a spatial learning task in a mouse model characterized by cognitive deficits of neurodevelopmental origin. Specifically, we used pERK immunostaining to study neuronal activation following Morris water maze (MWM, a classical hippocampal-dependent learning task) in Engrailed-2 knockout (En2-/-) mice, a model of autism spectrum disorders (ASD). As compared to wild-type (WT) controls, En2-/- mice showed significant spatial learning deficits in the MWM. After MWM, significant differences in the number of pERK-positive neurons were detected in specific hippocampal subfields of En2-/- mice, as compared to WT animals. Thus, our protocol can robustly detect differences in pERK-positive neurons associated to hippocampal-dependent learning impairment in a mouse model of ASD. More generally, our protocol can be applied to investigate the profile of hippocampal neuron activation in both genetic or pharmacological mouse models characterized by cognitive deficits.

We describe an immunohistochemistry protocol to study the profile of hippocampal neuron activation following exposure to a spatial learning task in a mouse model characterized by cognitive deficits of neurodevelopmental origin. This protocol can be applied to both genetic or pharmacological mouse models characterized by cognitive deficits.

Induction of phosphorylated extracellular-regulated kinase (pERK) is a reliable molecular readout of learning-dependent neuronal activation. Here, we ...

Using Single Sensillum Recording to Detect Olfactory Neuron Responses of Bed Bugs to Semiochemicals

The insect olfactory system plays an important role in detecting semiochemicals in the environment. In particular, the antennal sensilla which house single or multiple neurons inside, are considered to make the major contribution in responding to the chemical stimuli. By directly recording action potential in the olfactory sensillum after exposure to stimuli, single sensillum recording (SSR) technique provides a powerful approach for investigating the neural responses of insects to chemical stimuli. For the bed bug, which is a notorious human parasite, multiple types of olfactory sensillum have been characterized. In this study, we demonstrated neural responses of bed bug olfactory sensilla to two chemical stimuli and the dose-dependent responses to one of them using the SSR method. This approach enables researchers to conduct early screening for individual chemical stimuli on the bed bug olfactory sensilla, which would provide valuable information for the development of new bed bug attractants or repellents and benefits the bed bug control efforts.

Bed bugs rely on olfactory receptor neurons housed in their antennal olfactory sensilla to detect semiochemicals in the environment. Utilizing single sensillum recording, we demonstrate a method to evaluate bed bug response to semiochemicals and explore the coding process involved.

The insect olfactory system plays an important role in detecting semiochemicals in the environment. In particular, the antennal sensilla which house ...

Neuron-Macrophage Co-cultures to Activate Macrophages Secreting Molecular Factors with Neurite Outgrowth Activity

There is strong evidence that macrophages can participate in the regeneration or repair of injured nervous system. Here, we describe a protocol in which macrophages are induced to produce conditioned medium (CM) that promotes neurite outgrowth. Adult dorsal root ganglion (DRG) neurons are acutely dissociated and plated. After the neurons are stably attached, peritoneal macrophages are co-cultured on a cell culture insert overlaid on the same well. Dibutyryl cyclic AMP (db-cAMP) is applied to the co-cultures for 24 h, after which the cell culture insert containing the macrophages is moved to another well to collect CM for 72 h. The CM from the co-cultures treated with db-cAMP, when applied to a separate adult DRG neuron culture, exhibits robust neurite outgrowth activity. The CM obtained from the db-cAMP-treated cultures consisting of single cell type alone, either DRG neuron or peritoneal macrophage, did not exhibit neurite outgrowth activity. This indicates that the interaction between neurons and macrophages is indispensable for the activation of macrophages secreting molecular factors with neurite outgrowth activity into CM. Thus, our co-culture paradigm will also be useful to study intercellular signaling in the neuron-macrophage interaction to stimulate the macrophages to be endowed with a pro-regenerative phenotype.

The current protocol presents experimental procedures to stimulate cultured macrophages to be endowed with capacity to release molecular factors that promote neurite outgrowth. Treatment of cAMP to the neuron-macrophage co-cultures induces the macrophages to produce conditioned medium that possesses strong neurite outgrowth activity.

There is strong evidence that macrophages can participate in the regeneration or repair of injured nervous system. Here, we describe a protocol in which ...

Semi-Quantitative Determination of Dopaminergic Neuron Density in the Substantia Nigra of Rodent Models using Automated Image Analysis

Estimation of the number of dopaminergic neurons in the substantia nigra is a key method in pre-clinical Parkinson's disease research. Currently, unbiased stereological counting is the standard for quantification of these cells, but it remains a laborious and time-consuming process, which may not be feasible for all projects. Here, we describe the use of an image analysis platform, which can accurately estimate the quantity of labeled cells in a pre-defined region of interest. We describe a step-by-step protocol for this method of analysis in rat brain and demonstrate it can identify a significant reduction in tyrosine hydroxylase positive neurons due to expression of mutant &#945;-synuclein in the substantia nigra. We validated this methodology by comparing with results obtained by unbiased stereology. Taken together, this method provides a time-efficient and accurate process for detecting changes in dopaminergic neuron number, and thus is suitable for efficient determination of the effect of interventions on cell survival.

Here we present an automated method for semi-quantitative determination of dopaminergic neuron number in the rat substantia nigra pars compacta.

Estimation of the number of dopaminergic neurons in the substantia nigra is a key method in pre-clinical Parkinson's disease research. Currently, unbiased ...

In vivo Calcium Imaging of Mouse Geniculate Ganglion Neuron Responses to Taste Stimuli

Within the last ten years, advances in genetically encoded calcium indicators (GECIs) have promoted a revolution in in vivo functional imaging. Using calcium as a proxy for neuronal activity, these techniques provide a way to monitor the responses of individual cells within large neuronal ensembles to a variety of stimuli in real time. We, and others, have applied these techniques to image the responses of individual geniculate ganglion neurons to taste stimuli applied to the tongues of live anesthetized mice. The geniculate ganglion is comprised of the cell bodies of gustatory neurons innervating the anterior tongue and palate as well as some somatosensory neurons innervating the pinna of the ear. Imaging the taste-evoked responses of individual geniculate ganglion neurons with GCaMP has provided important information about the tuning profiles of these neurons in wild-type mice as well as a way to detect peripheral taste miswiring phenotypes in genetically manipulated mice. Here we demonstrate the surgical procedure to expose the geniculate ganglion, GCaMP fluorescence image acquisition, initial steps for data analysis, and troubleshooting. This technique can be used with transgenically encoded GCaMP, or with AAV-mediated GCaMP expression, and can be modified to image particular genetic subsets of interest (i.e., Cre-mediated GCaMP expression). Overall, in vivo calcium imaging of geniculate ganglion neurons is a powerful technique for monitoring the activity of peripheral gustatory neurons and provides complementary information to more traditional whole-nerve chorda tympani recordings or taste behavior assays.

Here we present how to expose the geniculate ganglion of a live, anesthetized laboratory mouse and how to use calcium imaging to measure the responses of ensembles of these neurons to taste stimuli, allowing for multiple trials with different stimulants. This allows for in depth comparisons of which neurons respond to which tastants.

Within the last ten years, advances in genetically encoded calcium indicators (GECIs) have promoted a revolution in in vivo functional imaging. Using ...

Modulation of the Neurophysiological Response to Fearful and Stressful Stimuli Through Repetitive Religious Chanting

In neuropsychological experiments, the late positive potential (LPP) is an event-related potential (ERP) component that reflects the level of one's emotional arousal. This study investigates whether repetitive religious chanting modulates the emotional response to fear- and stress-provoking stimuli, thus leading to a less responsive LPP. Twenty-one participants with at least one year of experience in the repetitive religious chanting of "Amitabha Buddha" were recruited. A 128-channel electroencephalography (EEG) system was used to collect EEG data. The participants were instructed to view negative or neutral pictures selected from the International Affective Picture System (IAPS) under three conditions: repetitive religious chanting, repetitive nonreligious chanting, and no chanting. The results demonstrated that viewing the negative fear- and stress-provoking pictures induced larger LPPs in the participants than viewing neutral pictures under the no-chanting and nonreligious chanting conditions. However, this increased LPP largely disappeared under repetitive religious chanting conditions. The findings indicate that repetitive religious chanting may effectively alleviate the neurophysiological response to fearful or stressful situations for practitioners.

The present event-related potential (ERP) study provides a unique protocol for investigating how religious chanting can modulate negative emotions. The results demonstrate that the late positive potential (LPP) is a robust neurophysiological response to negative emotional stimuli and can be effectively modulated by repetitive religious chanting.

In neuropsychological experiments, the late positive potential (LPP) is an event-related potential (ERP) component that reflects the level of one's ...