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Neuroexplorer 4

Manufactured by Plexon
Sourced in United States

NeuroExplorer 4 is a software application designed for the analysis of neural data. It provides tools for visualizing, processing, and analyzing electrophysiological recordings from various sources, including single-unit activity, local field potentials, and electroencephalography (EEG) data.

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7 protocols using neuroexplorer 4

1

Spinal Cord Neuronal Recording Protocol

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A four-electrode array with a total of 16 recording sites (A4 type, NeuroNexus) was implanted at the L5 spinal level. The array was oriented so that each electrode was at the same mediolateral position. Electrode tips were lowered 328 ± 95 μm (mean ± SD) below the dorsal surface. Since recording sites are spaced at 50 μm intervals up each electrode, we determined on which site a unit was recorded and from this measured the depth of recorded neurons to be <300 μm (see Figure 3C), which places them within lamina I or II (Watson et al., 2008 (link)). Neurons that responded to limb displacement, indicating proprioceptive input, were excluded. The signal was amplified, filtered at 500 Hz – 10 kHz, digitized at 20 kHz with an Omniplex Data Acquisition System (Plexon) and stored with stimulus markers on disk. Single units were isolated using Offline Sorter V3 software (Plexon), and were analyzed with Neuroexplorer 4 (Plexon). Spike waveforms were identified as monophasic or biphasic based on the absence or presence, respectively, of a negative phase (upward deflection) following the initial positive phase (see Figure 2A).
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2

Multicontact Electrode Recording of Neural Oscillations

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After anesthesia with pentobarbital sodium (50 mg/kg, intraperitoneally), mice were placed in a stereotaxic apparatus (Stoelting, USA) and subjected to craniotomy (8 mm × 10 mm). Electrophysiological recordings were conducted by linear array multicontact U-Probe electrodes (PLX-UP-16-16ED-50-260-40-20(640)-15T-900-C16o25, U-Probe-Item 33574-50, Plexon, USA) containing 16 recording contacts (0.3–1.3 MΩ at 1 kHz) with an intercontact spacing of 50 μm to obtain spell out (local field potentials [LFP]) in vivo. Data were analyzed off-line using software from Offline Sorter V3, Neuroexplorer 4 (Plexon) and MATLAB 7.5 software by MathWorks. The low and high gamma bands were set at 35 to 55 and 65 to 110 Hz, respectively. Theta oscillations were extracted by applying a 4 to 12 Hz finite impulse response passband with zero-phase shift filter function in MATLAB (Supplementary Materials and Methods).
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3

Automated Sleep Spindle Detection

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Sleep spindles were analyzed using Clampfit 10.2 (Axon Instruments) and NeuroExplorer4 (Plexon) in the wake and NREM sleep stages and detected using the following complementary method: the EEG time series were bandpass-filtered in the frequency range of 7–15 Hz, and signal was computed in moving windows of 1 s duration and at 0.01 s intervals. Sleep spindles were detected during those times in which the root mean square (rms) value of the filtered signal exceeded its 85th percentile, as previously suggested (Dang-Vu et al., 2010 (link)). Detected spindles with durations lower than 0.5 s or longer than 5 s were discarded. To estimate spindle density (SD) during a given sleep stage, all spindles were counted and the total number was divided by the total recording time.
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4

Multielectrode Neurophysiological Recording Techniques

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Extracellular single-unit and local field potentials (LFPs) recordings were obtained from an implanted intracranial multielectrode array structure. The 16-channel multielectrode array was connected to a wireless high-frequency headstage transmitter (W16; Triangle Biosystems, Durham, NC, USA) that sent continuous analog signals to a Multineuron Acquisition Processor system (16MAP, Plexon Inc., Dallas, TX, USA). Neural signals were preamplified (10,000–20,000X) and digitized at 40 kHz. Voltage-time threshold windows were used to identify single-unit waveforms online (SortClient 2.6; Plexon) and validated offline using automatic and manual sorting techniques (Offline Sorter 2.8; Plexon Inc., Dallas, TX, USA) according to the cumulative criteria described in detail previously [33 (link)]. Extracellular LFFs signals were obtained by low-frequency (0.2–200 Hz) filtering of the raw signals. LFPs were preamplified and digitized at a 0.5 kHz sampling rate. These data were subsequently processed offline using the NeuroExplorer 4 software (NEX 4, Plexon Inc., Dallas, TX, USA) and exported to MatLab (R17, MathWorks, Natick, MA, USA) to be further analyzed using custom routines.
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5

Sleep Pattern Analysis in Mice

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The data were collected and processed randomly. All immunocytochemistry and behavioral tests were carried out blind. The electrophysiology experiments were not blind, but data collection and analyses were performed blind. Sample size was calculated according to the preliminary experiment results and the following formula: N=[(Zα/2+Zβ)σδ]2(Q11+Q21) , where α = 0.05 significant level, β = 0.2, power = 1-β, δ is the difference between the means of two samples, and Q is the sample fraction. The samples were randomly assigned to each group. The data were presented as mean ± SEM. One-way ANOVA was used for analysis of electrophysiological data in vitro. Two-tailed Student’s t-tests were performed after the normality test for the data from all groups in vivo. Variance was similar between groups being compared. We considered p < 0.05 to be statistically significant. The sleep patterns were determined by combined EEG, EMG, and video recordings. Data were presented as mean ± SEM. All data were analyzed using Origin8.0 (OriginLab), Clampfit 10.2 (Axon Instruments), NeuroExplorer4 (Plexon), and Microsoft Excel 2010. Data were exported into Illustrator CS6 (Adobe Systems) for preparation of figures.
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6

Spinal Cord Neuron Recording Protocol

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A 4-shank probe with a total of 16 recording microelectrodes (A4 × 4–3mm-50-125-177-A16, NeuroNexus, Ann Arbor, MI, USA) was implanted at the L5 spinal level in the left DH. The array was oriented parallel to the rostrocaudal axis so that each electrode was at roughly the same mediolateral position. The depth of electrode insertion was monitored to estimate electrode position within the presumed Rexed lamina(e).
Electrode shank tips were lowered below the dorsal surface. Since the recording sites were spaced at 50 µm intervals up each shank of the electrode, we estimated the depth of the recorded neurons to be positioned within lamina II–III. Neurons that responded to limb displacement, indicating that they received proprioceptive input, were excluded. Measured extracellular signals of neuronal activity were amplified, and the band-pass was filtered between 500 Hz and 10 kHz, digitized at 40 kHz with the OmniPlex Data Acquisition System (Plexon, Dallas, TX, USA), and stored with stimulus markers on a disk. Single units were isolated using Offline Sorter v3 software (Plexon, Dallas, TX, USA) and analyzed with NeuroExplorer 4 (Plexon, Dallas, TX, USA).
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7

Spinal Cord Neuronal Recordings

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A 4-shank probe with a total of 16 recording microelectrodes (A4x4-3mm-50-125-177-A16, NeuroNexus) was implanted at the L5 spinal level in the left DH. The array was oriented parallel to the rostrocaudal axis so that each electrode was at roughly the same mediolateral position. Depth of electrode insertion was monitored to estimate electrode position within presumed Rexed lamina(e). Electrode shank tips were lowered 354 ± 87 μm (mean ± standard deviation) below the dorsal surface. Since recording sites are spaced at 50 μm intervals up each shank of the electrode, we estimated the depth of recorded neurons to be positioned within lamina I or II. Neurons that responded to limb displacement, indicating that they received proprioceptive input, were excluded. Measured extracellular signals of neuronal activity were amplified, band-pass filtered between 500 Hz and 10 kHz, digitized at 40 kHz with OmniPlex Data Acquisition System (Plexon, Dallas, TX, USA), and stored with stimulus markers on disk. Single units were isolated using Offline Sorter v3 software (Plexon) and were analyzed with NeuroExplorer 4 (Plexon).
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