Meaning of Spike Viewer Graphs

[Michael Loftus]

I've started to explore the OpenEphys GUI with the stereotrode example data that comes with it, and I have some questions about the Spike Viewer.  It looks like it's performing PCA for spike-sorting, but I haven't found any documentation that explicitly clarifies this.  Would you be able to answer a few questions for me?

 - How does what's displayed on the waveform viewer relate to the raw signal?  If I'm not mistaken, each electrode on the stereotrode has only one channel, so I would only expect one waveform. Why are there five waveforms displayed in the waveform viewer?  Are these the principal components used to sort the spikes?

 - What is the x-axis on the waveform viewer and what are its units?

 - What is the y-axis on the peak viewer, and what are the units for the x- and y-axes on the peak viewer?  The x-axis appears to be spike amplitude.

If you know of any good resources for further reading, I'd appreciate those as well!

Best,

Michael Loftus

[Josh Siegle]

Hi Michael,

The points in the "peak view" represent the peak amplitudes for each spike on the two channels of the stereotrode (ch1 vs ch2). The scale of each axis matches what's shown in the two channels of the waveform view. The default is 250 microvolts, but you can cycle through different options for this.

The waveform view shows the five most recent spike waveforms detected on each channel. The two channels in each stereotrode are acquired together whenever a threshold crossing is detected on one of them. 

The x-axis scale of the waveform view depends on the sample rate of your data source. Each spike contains 40 samples, so for a 30 kHz sample rate that would represent 1.3 ms.

You can find more info about the Spike Viewer here: https://open-ephys.github.io/gui-docs/User-Manual/Plugins/Spike-Viewer.html

In contrast to the Spike Viewer, the Spike Sorter *does* calculate the principal components for each waveform. That plugin is used to perform real-time spike sorting on the outputs of the Spike Detector using manually drawn boundaries in waveform or PCA space. That plugin is documented here: https://open-ephys.github.io/gui-docs/User-Manual/Plugins/Spike-Sorter.html

Josh

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