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Spike2 software is a data acquisition and analysis tool for electrophysiology research. It provides a comprehensive set of features for recording, visualizing, and analyzing neural signals, such as spikes, local field potentials, and analog waveforms. The software supports a wide range of data acquisition hardware, enabling users to capture and process electrophysiological data from various experimental setups.

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564 protocols using spike2

1

Pelvic Nerve Afferent Recording

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One of the pelvic nerves was positioned in a glass fire-polished tip (tip opening, ∼100 μm) of a suction electrode using negative pressure. Action potentials recorded from the pelvic nerve were collected using a Neurolog headstage (NL100AKS; Digitimer, Hertfordshire, UK), amplified with an AC preamplifier (NL104; Digitimer), and band-pass filtered at 200–4,000 Hz (NL125/NL126; Digitimer) to remove noise. Data were collected and stored using a Power 401 analog-to-digital interface and Spike 2 software (Cambridge Electronic Design, Cambridge, UK). Pressure was acquired at a rate of 100 Hz, and afferent activity was acquired at a rate of 25,000 Hz. The threshold for detecting afferent nerve activity was set at twice the root mean square of the recorded signal in the absence of action potentials, a level well-above signal noise. Bladder pressure and afferent nerve activity were recorded simultaneously and analyzed offline using Spike 2 software (Cambridge Electronic Design). Action potential frequency was calculated from detected action potentials. “Afferent activity” was defined as the number of action potentials per second (Hz).
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2

Extracellular and Intracellular Recordings of Pharyngeal Nerves and Muscles

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Extracellular recordings of pharyngeal nerves (AN, MN and PaN) and intracellular recordings of the CDM were performed as previously described in [20 (link)]. In brief, for extracellular recordings of pharyngeal nerves, each nerve was electrically isolated using a petroleum jelly pool surrounding the nerve placed on a piece of Parafilm. Silver wire electrodes were used for measuring with differential recordings motor output of the deafferented nerve. A preamplifier (Model MA103, Ansgar Büschges group electronics lab) connected to a four-channel amplifier/signal conditioner (Model MA 102, Ansgar Büschges group electronics lab) was used. All recorded signals were amplified (amplification factor: 5000) and filtered (bandpass: 0.1–3 kHz). Recordings were sampled at 20 kHz. Data was acquired with Micro3 1401 or Power 1401 mk2 A/D board (Cambridge Electronic Design) and Spike2 software (Cambridge ElectronicDesign). Intracellular muscle recordings of the CDM were recorded using glass microelectrodes filled with 3 M KCl solution (tip resistance: 20–30 MΩ) connected to an intracellular amplifier (BRAMP-01R, npi electronic GmbH). All recordings were digitally sampled by a Power 1401 mk2 A/D board (Cambridge Electronic Design) at 20 kHz. Data was acquired with Spike2 software (Cambridge Electronic Design).
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3

Murine Atrial Action Potential Recordings

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Transmembrane murine atrial action potentials (TAP) were recorded as published (Lemoine et al., 2011 (link)) immediately before or after the optical mapping procedure. TAPs were recorded from isolated superfused LA samples prepared as above using borosilicate glass microelectrodes (tip resistance 15–30 MΩ), filled with 3 M KCl. Voltage signals were amplified (Axoclamp 2B; Molecular Devices, USA), digitised and displayed using spike2 software (Cambridge Electronic Design, UK). The sampling frequency was 20 kHz. Preparations were paced successively (300 ms–80 ms) with platinum electrodes at twice the diastolic voltage threshold, with a minimum of 50 APs recorded at each cycle length using an isolated constant voltage stimulator (Digitimer, UK) driven by an analogue to digital converter with spike2 software (Cambridge Electronic Design, UK). Measurements of APD and intra-atrial activation times were obtained using custom-made spike2 algorithms.
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4

Odor Discrimination in Rats

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Odor discrimination was assessed in a two-alternative odor discrimination task (Fig. 1A). Animals received 30 min training sessions 5 days per week. The operant chamber was described previously in (Chapuis and Wilson 2011 (link); Courtiol and Wilson 2016 (link)). In brief, it consisted of a plexiglas box with a central odor port on the central wall and two goal ports on the left and right walls (Vulintus). A trial was initiated by a nose poke into the central port which triggered the delivery of an odor terminating when the rats withdraw their nose from the central port. Rats were required to hold in the odor port for at least 0.3 s for the event to be considered a trial eligible for a reward. Water reward (~35μl) was delivered, depending on odor identity, upon a correct choice of the left or right goal port within 3 s. The operant chamber was controlled by Spike2 software (Cambridge Electronic Design) and all behavioral epochs were recorded through Spike2.
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5

Optogenetic Manipulation of Prefrontal Cortex

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The experimental protocol is the same as in Dilgen et al. (2013 (link)) and Oprisan et al. (2015 (link)). Briefly, male PV-Cre mice (B6; 129P2 – Pvalbtm1(Cre)Arbr/J Jackson Laboratory (Bar Harbor, ME, USA) were infected with the viral vector (AAV2/5. EF1a. DIO. hChR2(H134R) – EYFP. WPRE. hGH, Penn Vector Core, University of Pennsylvania) delivered to the mPFC as described in detail in Dilgen et al. (2013 (link)). The extracellular signals were amplified using a Grass amplifier (Grass Technologies, West Warwick, RI, USA), digitized at 10 kHz by a 1401plus data acquisition system, visualized using Spike2 software (Cambridge Electronic Design, LTD., Cambridge, UK) and stored on a PC for offline analysis. A HumBug 50/60 Hz Noise Eliminator (Quest Scientific Inc., Canada) filter canceled out the line noise and the signal was band-pass filtered online between 0.1 and 130 kHz to obtain the LFPs. A 473 nm laser (DPSS Laser System, OEM Laser Systems Inc., East Lansing, MI, USA) delivered the light stimulation via a 1401plus digitizer and Spike2 software (Cambridge Electronic Design Ltd., Cambridge, UK).
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6

Electrophysiological Monitoring of Rodent Behavior

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After one week of recovery from surgery, animals were habituated in the recording cage (white plexiglass of 12′′ × 12′′ × 11′′ length, width, and height). The recording cage was placed in a well-ventilated, sound and light dampened (black color plexiglass) recording chamber (48′′ × 24′′ × 24′′) to minimize external disturbances during the experiments. The recording chamber was illuminated with 20 Lux light. Food and water bottle were placed in the food cup and bottle holder attached to the recording cage. Animals were tethered with the recording cable through a commutator and habituated to the recording chamber for 6 hrs (11:30 AM–5:30 PM) on two consecutive days. Also, during this period, the EEG and EMG signals were examined in a computer through Spike2 software (Cambridge Electronic Design, Cambridge, UK). EEGs were recorded in two channels and EMG was recorded in a single channel. Electrophysiological signals were amplified using 15LT Bipolar Portable Physiodata Amplifier System (Astro-Med, USA). EEG signals were processed with a high-pass filter of 0.1 Hz and a low-pass filter of 40 Hz, while EMG signal was processed with a high-pass filter of 10 Hz and a low-pass filter of 90 Hz digitized at 100 Hz sampling rate. Recordings were acquired in a personal computer using Spike2 software (Cambridge Electronic Design, Cambridge, UK) and were saved for offline analysis.
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7

Quantifying Lower Limb Muscle Activity

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Surface electromyography (EMG) was performed using three Trigno Wireless electrode sensors (Delsys Inc. Ltd. Boston, United States), which had a predetermined bandwidth of 20–450 Hz, a gain of 1,000, a common-mode rejection ratio of >80 dB, and a sampling rate of 2,000 Hz. After standard skin preparation, the electrodes were placed over the MG, SOL and Tibialis anterior (TA) according to SENIAM guidelines (Hermens et al., 1999 (link)). The EMG signals were collected at a sampling rate of 2,100 Hz and stored for offline analysis. All EMG data were visually inspected prior to analysis. EMG data for each gait cycle were exported from Visual 3D and imported into Spike2 software (Cambridge Electronic Design, Cambridge, United Kingdom) for further analysis. EMG raw signals were notch filtered at 50 Hz (to remove ambient noise from power supply), rectified and smoothed using a 5-point moving average (Spike2, Cambridge Electronic Design, Cambridge, United Kingdom). The EMG amplitude for each muscle was calculated as root mean square (RMS) over five stance cycles (initial contact to toe-off).
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8

Nerve Activity Measurement Methodology

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In order to obtain a measure of nerve activity, the trace recorded in Spike 2 (Cambridge Electronic Design) was first duplicated to apply different filtering processes to the A and C fibre CAPs. A fibre CAP signals were filtered within Spike2 using DC removal at 20 ms time constant and smoothing at 100 μs time constant to remove DC offset and high-frequency noise, respectively. Conversely C fibre CAP signals were filtered using DC removal at 20 ms time constant and smoothing at 900 μs time constant respectively. Additionally, stimulation artifacts were digitally blanked in MATLAB (Mathworks) to produce the plots shown in Figure 3. For statistical analysis CAP signals were rectified and integrated in MATLAB to produce a value representing neural activity in response to stimulation. Measures of activity reported in Figures 4, 5 are reported as relative to the baseline activity of 1, comparing activity at start of trials with activity measured during the trial, such as in the block or recovery phases. Signal filtering was carried out in Spike2 (Cambridge Electronic Design) and rectification-integration analysis and plotting were carried out using MATLAB (Mathworks).
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9

Nerve Spike Analysis Protocol

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Data were digitized and stored onto a computer hard disk through an appropriate interface (Power1401) and software (Spike2) from Cambridge Electronic Design Ltd. (Cambridge, UK).
Data were analyzed using the Spike2 analysis software. Spikes recorded from the CBCO nerve were identified according to their waveform based on a template matching protocol (wavemark). Templates were built automatically and corresponded to the mean duration of sensory spikes (about 1.5 ms in duration). The sampling rate for CBCO nerve recording was set to 15 kHz, which resulted in templates containing 20–22 points. The procedure used two criteria to identify a spike: (1) more than 90% of the points should be in the confidence limits of the template and (2) the maximum amplitude change for a match was less than 5%. This procedure was applied off-line. After the completion of this protocol, each identified CBCO unit (spike shape) was assigned an arbitrary number. Subsequently, a spike triggered average was performed for each CBCO unit, allowing us to observe in a given MN the occurrence of any postsynaptic events related to this unit.
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10

Assessing Motor Function with Smartphone Sensors

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A smart device (iPod Touch 5th generation, iOS 12.11, Apple Inc., CA) and data logging App (Sensor Data, Wavefront Labs) recorded the outcomes for the motor battery tasks. Research assistants described and demonstrated each task briefly and provided reminders of technique between tasks. Each task was completed twice, with a rest period of 30s between trials. Data were transferred to a lab computer and imported into the Spike 2 software program (Spike 2, v. 7.14, Cambridge Electronic Design, Cambridge, UK) for visual inspection and analysis. Motor BatterySupplementary Material provide materials, setup, and processing details for all tasks.
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