spikeExtractionTetrodeTrialByTrial: Perform the spike extraction for a given tetrode, reading...

Description Usage Arguments Details

View source: R/SpikeExtraction.R

Description

This function uses much less memory, especially if the recording session is very long.

Usage

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spikeExtractionTetrodeTrialByTrial(rs, df, tetrodeNumber, minPassHz = 800,
  maxPassHz = 5000, powerWindowSizeMs = 0.4, powerWindowSlideMs = 0.1,
  SDThreshold = 2, simultaneousSpikeMaxJitterMs = 0.2,
  spikeDetectionRefractoryMs = 0.5, waveformWindowSizeMs = 1,
  firstSample = 0, lastSample = -1)

Arguments

rs

RecSession object

df

DatFile object

tetrodeNumber

Tetrode number. Index starts at 1.

minPassHz

Minimal frequency in Hz that is kept before calculating power

maxPassHz

Maximal frequency in Hz that is kept

powerWindowSizeMs

Size in ms of the sliding window to calculate power

powerWindowSlideMs

Shift of the power window between calculation of power

SDThreshold

Power threshold in standard deviation above the mean for detection of a spike

simultaneousSpikeMaxJitterMs

Use to join spikes detected on several channels

spikeDetectionRefractoryMs

Period of refractory in the detection of spikes

waveformWindowSizeMs

Window size used when extracting the spike waveforms.

firstSample

First sample to consider in spike detection, by default 0, indices start at 0

lastSample

Last sample to consider in spike detection, if not set by user, all samples will be used

Details

A RecSession object is used to get the information about the assignation of the recorded channels to tetrodes and the file names. For each channel of the tetrode, the raw signal is band pass filtered and the power is estimated with the root mean square in sliding windows. Baseline variation in power are estimated by the standard deviation of power. Time windows above a threshold contain a spike. The spike times are aligned to the most negative value within the adjacent windows with power above the threshold. The spike times in sample number are saved in sessionName.res.tetrodeNumber. The spike waveforms are saved in binary format in sessionName.spk.tetrodeNumber. The features of spikes are obtained via principal component analysis and 3 features are kept for each channel. The spike features are saved in sessionName.fet.tetrodeNumber.


kevin-allen/relectro documentation built on May 20, 2019, 9:06 a.m.