Shank Viewer

Feature Quick Reference

Data Flow

Raw data -> Fetcher -> Graphs -> Shank

Every tenth of a second a process thread called the 'graph fetcher' grabs the next chunk of raw data from the main data stream and pushes it to the Graphs window. The stepping of the visible time cursor across the screen heralds these events.

If the corresponding Shank Viewer is visible, the Graphs window pushes a copy of the unmodified raw data chunk to the Shank Viewer. Importantly, the filter choices in the Graphs window do not affect the Shank Viewer; each does its own filtering/processing.

Note that clicking Pause in the Graphs window pauses/resumes both the graphs and the shank activity mapping.

The Shank Viewer applies a 300Hz highpass filter to AP band channels and a 0.2Hz - 300Hz bandpass filter to the LFP channels. These filters reduce out-of-band electrical noise, including DC offsets, which allows better comparison to your requested spike threshold voltage.

Setting a Spike Threshold

You can read an appropriate threshold level from a graph:

  1. Select a graph and double-click to blow it up.
  2. Turn off all filters except -<T> (approximates Shank View filtering).
  3. Mouse over the graph; read the voltage in the status bar.
  4. Be conservative, set a value ~75% of the peak.

Setting 'Stay low'

This value gives you a rough spike width filter. Our spike detection logic requires that the signal cross the threshold (from high to low) and continuously stay low for at least this many samples.

Unfortunately, if you've got a lot of electrical noise, the signal could cross back and forth rapidly across the threshold. The detector thinks such spikes are narrow and they are rejected if 'stay low' is too high.

If your spike rates seem too low, try lowering 'stay low'.

To directly examine the noise in a selected graph:

  1. Double-click to blow it up.
  2. Set a very fast time scale like 0.01s for better resolution.
  3. Use the Pause button to freeze the display for a better look.