spikeExtractionSession: Perform the spike extraction for a recording session
In kevin-allen/relectro: Analysis of electrophysiological data

This function does the spike extraction for a recording sessions. A RecSession object is used to get the information about the assignation of the recorded channels to tetrodes and the trial names.

spikeExtractionSession(rs, minPassHz = 800, maxPassHz = 8000,
  powerWindowSizeMs = 0.3, powerWindowSlideMs = 0.1, SDThreshold = 2.25,
  simultaneousSpikeMaxJitterMs = 0.2, spikeDetectionRefractoryMs = 0.5,
  waveformWindowSizeMs = 1, firstSample = 0, lastSample = -1)

`rs`	RecSession object
`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 on a single channel
`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

The extraction is done trial by trial (each dat file separately). A band pass filter (Butterworth filter) is applied to the raw signal. The power (root mean square) is calculated in sliding windows to obtain the mean and standard deviation of the power. A threashold is set for spike detection. Adjacent windows above threshold contain one spike, a sholder of the spike refractory period is added to the window. The spike time is assigned to the most negative value in the window. After detecting spikes on all channels of a tetrode, the spikes occurring almost simultaneously on different channels are merged. The spike waveforms are extracted and the waveforms recorded on the same channels are submitted to a principal component analysis. The first 3 components of each channels are used as spike features.

First tested with simulated spikes (see simulateRawTrace() and spikeDetectionAccuracy()). There is a testthat file showing how this is done (test/testthat/test_SpikeTrain.R).

Then tested against the procedure used from JC with recordings from the medial entorhinal cortex. Spikes with large amplitude are detected by both methods. There is more variability between methods when spikes are close to detection threshold. This method with the default parameters have a shorter detection refractory period after a spike.

You can have a visual inspection of the spike detection with plotSpikeDetectionSegment().

The spike times of a tetrode are saved in sessionName.res.tetrodeNo. The spike features are saved in sessionName.fet.tetrodeNo. The spike waveform (in binary format) are saved in sessionName.spk.tetrodeNo.

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