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Offline sorter program

Manufactured by Plexon
Sourced in United States

Offline Sorter is a software program designed for the analysis and sorting of neural data. It provides users with tools to view, analyze, and sort waveforms from recorded neural signals. The program allows users to perform spike sorting and other data processing tasks on recorded neural data files.

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6 protocols using offline sorter program

1

Non-matching Sample Task in Monkeys

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The monkeys were trained to perform DNMS task for 3 h/day, 5 day/week. The monkeys reached a 96% correct-response rate after 3 months of training23 (link)27 (link). After completion of this training period, a head-restraining device, which was a U-shaped plate made of epoxy resin, was attached to the skull under aseptic conditions23 (link)27 (link). After the monkeys relearned the DNMS task and were correct at least 85% of the time, we commenced recording neuronal activity from each hemisphere in both subjects. A glass-insulated tungsten microelectrode (0.8–1.5 MΩ at 1 kHz) was stereotaxically inserted into the pulvinar vertically to the orbitomeatal plane. The analog signals of the neuronal activities, visual stimulus triggers, juice rewards, button presses, and X-Y eye position coordinates were digitized at a 40-kHz sampling rate and stored in a computer through a multichannel acquisition processor (Plexon Inc., Dallas, TX) system. The digitized neuronal activities were isolated into single units by their waveform components with the Offline Sorter program (Plexon Inc.). The data that were used in the present study were previously reported in Le et al. (2013, 2014)23 (link)27 (link), and more details of the procedures can be found in those studies.
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2

Electrophysiological Recording Protocol

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We used the same procedures previously described in Gullo et al. (2009 (link), 2010 (link)). Briefly, analog signals sampled at 40 kHz were recorded at 36°C in CO2-controlled incubators using MEA-1060BC or 1060INV pre-amplifiers (bandwidth 1–8000 Hz, Multichannel Systems, Germany) connected to a MEA Workstation (bandwidth 100–8000 Hz, Plexon Inc., USA). Data were sorted into timestamp files by the MEAWorkstation Sorter software (MEAWS, see details below) and cleaned of artifacts using the OFFLine Sorter program (Plexon Inc., USA). Next, during the PCA-based waveform sorting and for multi-unit electrodes, we applied one of the following procedures: (i) spike removal with a Mahalanobis threshold in the range 1.8–1.4; we concurrently checked that the P-value of multivariate ANOVA sorting quality statistics was <0.01 amongst the identified units; (ii) when the previous procedure led to excessive spike invalidation, we manually removed the spikes invading the adjacent unit ellipsoids (the latter method was very effective in decreasing the P-values, with only a limited number of erased spikes).
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3

Neuronal Activity During DNMS Task

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After the monkeys relearned the DNMS task at a rate greater than 85% correct, we commenced daily recording of neuronal activity during the DNMS task. Neuronal activity was recorded from each hemisphere in both subjects. A glass-insulated tungsten microelectrode (0.8–1.5 MΩ at 1 kHz) was stereotaxically inserted into the pulvinar vertically to the orbitomeatal plane in a stepwise fashion by a pulse motor-driven manipulator (SM-21; Narishige Scientific Instrument Lab, Tokyo, Japan). Only neuronal activities with a signal-to-noise ratio greater than 3∶1 were recorded. The analog signals of the neuronal activities, the triggers for visual stimuli, juice rewards, button pressing, and the X-Y coordinates of eye position were digitized at a 40-kHz sampling rate and stored in a computer through a multichannel acquisition processor (MAP; Plexon Inc., Dallas, TX, USA) system. The digitized neuronal activities were isolated into single units by their waveform components using the Offline Sorter program (Plexon Inc.). Superimposed waveforms of the isolated units were drawn in order to assess the variability throughout the recording sessions and then transferred to the NeuroExplorer program (Nex Technologies, Littleton, MA, USA) for further analysis.
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4

Neuronal Activity Recordings from Monkey Brain

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The monkeys were trained in the delayed nonmatching-to-sample task for 3 h/day, 5 days/week. After completion of this training period, a head-restraining device, which was a U-shaped plate made of epoxy resin, was attached to the skull under aseptic conditions (Nguyen et al., 2013 (link), 2014 (link)). After the monkeys relearned the delayed nonmatching-to-sample task and were correct at least 85% of the time, we commenced recording neuronal activity from each hemisphere in both subjects. A glass-insulated tungsten microelectrode (0.8–1.5 MΩ at 1 kHz) was stereotaxically inserted into the SC and pulvinar vertically to the orbitomeatal plane. The analog signals of the neuronal activities, visual stimulus triggers, juice rewards, button presses, and X-Y eye position coordinates were digitized at a 40-kHz sampling rate and stored in a computer through a multichannel acquisition processor (Plexon Inc., Dallas, TX) system. The digitized neuronal activities were isolated into single units by their waveform components with the Offline Sorter program (Plexon Inc.). The data that were used in the present study were previously reported in Nguyen et al. (2013 (link), 2014 (link)), and more details of the procedures can be found in those studies.
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5

Single Unit Recordings in Frontal Cortex

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After training, we surgically placed a recording chamber centered over area 45 and FEF on the right hemisphere of the animal. Single units were recorded using tungsten microelectrodes (2–4 MΩ) that were under the control of a microdrive. Electrodes were inserted through a guide tube positioned and lowered to just above the surface of the dura mater. Electrophysiological data were collected using the TDT system (Tucker & Davis) at a sampling rate of 1-kHz. Action potentials were amplified, filtered, and discriminated conventionally with a time-amplitude window discriminator. Spikes were isolated online if the amplitude of the action potential was sufficiently above background to reliably trigger the time-amplitude window discriminator, the waveform of the action potential was invariant throughout experimental recording, and the isolation could be sustained for sufficient period of recording. The identification and isolation of individual spikes was reevaluated and corrected offline using three-dimensional PCA and visual inspection of selected waveforms (Offline Sorter Program, Plexon .Inc) to ensure only single units were included in subsequent data analysis.
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6

Multichannel Spike Sorting and Artifact Removal

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We used the same procedures previously described in Gullo et al. (2009 (link), 2010 (link)). Briefly, analog signals sampled at 40 kHz were recorded at 36°C in CO2-controlled incubators using MEA-1060BC or 1060INV pre-amplifiers (bandwidth 1–8,000 Hz, Multichannel Systems, Germany) connected to a MEA Workstation (bandwidth 100–8,000 Hz, Plexon Inc., USA). Data were sorted into timestamp files by the MEAWorkstation Sorter software (MEAWS, see details below) and cleaned of artifacts using the OFFLine Sorter program (Plexon Inc., USA). Next, during the PCA-based waveform sorting and for multi-unit electrodes, we applied one of the following procedures: (i) spike removal with a Mahalanobis threshold in the range 1.8 to 1.4; we concurrently checked that the P-value of multivariate ANOVA sorting quality statistics was <0.01 among the identified units; (ii) when the previous procedure led to excessive spike invalidation, we manually removed the spikes invading the adjacent unit ellipsoids (the latter method was very effective in decreasing the P-values, with only a limited number of erased spikes).
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