Spike Plots

This section will cover spike plots and their properties.  Some plot properties are based on spike window settings.  For more information on window specific settings (including adding plots to windows) see the spike window overview.


Spike Plot Overview

1. Plot Title Bar The title bar houses the name of the acquisition entity whose data is displayed in the plot, along with the user defined plot label, if one was set.  If the plot is the currently selected plot for the window it is in, the title bar will be purple.  Along the right hand side, you will see icons that represent actions that can be applied to the entire plot, regardless of the current  plot type.
2. Waveform Plot Here is where the spike waveforms will be shown.  Single electrodes will only have a single waveform.  Stereotrodes will have two (channel 1 on the left, channel 2 on the right); and tetrodes (shown above) will have four (channel 1 on the top left, channel 2 on the top right, channel 3 on the bottom left, channel 4 on the bottom right).  See the detailed description of the waveform plot for more information.  If a channel of the acquisition entity is disabled,the waveform plot will change to show that the channel is disabled as shown in the following image:


If the waveform plot is too small, the DISABLED text will not be visible.  Once the channel is enabled, it will display data normally.
3. Feature Plot The feature plot is a configurable XY scatter plot of values calculated from detected spikes.  The number of feature plots that are shown can be configured separately for maximized and normal views.See the detailed description of the feature plot for more information.
4. Previous Plot This option is only available when the plot is in the maximized view.  Clicking on it will switch the currently displayed plot to the previous plot in the window.  If this is the first plot in the window, clicking this icon will have no effect.
5. Next Plot This option is only available when the plot is in the maximized view  Clicking on it will switch the currently displayed plot to the next plot in the window.  If this is the last plot in the window, clicking this icon will have no effect.
6. Maximize/Restore Plot Toggles the view for the plot.  If the plot is in maximized view (shown above), clicking this icon will restore the plot to normal view (showing all plots in the window).  When in normal view, the icon changes to a single square, and clicking on it will maximize the plot whose icon is clicked.
7. Clear Window Clears all data in this plot only.  This can also be accomplished by right clicking on the plot and selecting Clear Plot from the menu.
8.  Plot Properties Clicking this icon will make the properties page visible, select the display tab, and select the plot in the properties tree.  This can also be accomplished by right clicking anywhere on the plot and selecting Plot Properties from the menu.  See the detailed description of spike plot properties for more information on plot properties.
9. Audio Menu Displays the audio menu .


Waveform Plot

Each channel of a spike acquisition entity (AE) will have its own waveform plot.  Here we are looking at a single electrode waveform plot.

1. Input Range Displays the current input range of this channel in microvolts.  Any waveform that reaches the top of the plot will have a voltage value approximately equal to this value.  The bottom of the plot represents the negative of this value.
2. Spike Detection Value Bar This bar is positioned in the plot to give an approximation of the current spike detection voltage (in microvolts) for this channel.  Clicking and dragging this bar up and down will adjust the spike detection voltage for this channel accordingly.  The value that is adjusted and shown depends on the method of spike detection used for this acquisition entity.  This functionality is not available when __prod_name is recording.
  1. Threshold: The spike detection value is the threshold voltage used to determine if an incoming signal should be classified as a spike.  The bar will look like the following when in threshold mode: 
  2. Slope:   The spike detection value is the change in voltage used in calculating the slope to use for detecting spikes.  This bar does not indicate, nor does dragging it affect, the change in time portion of the slope.  The bar will look like the following when in slope mode: 
3. Spike Waveform The waveform of detected spikes.  If the window is in overlay mode, spikes will accumulate as they are detected; otherwise all spikes detected since the last screen refresh will be shown.  When cells are defined for this AE, waveforms will appear in the color of their corresponding cell.  If the detected spike does not have a defined cell, it will appear in gray.
4.  Zero Line This represents the zero (0) value line in microvolts of the spike waveform.  Depending on the selection value of the Input Inverted option, positive and negative voltages are either above or below this line.
5.  Spike Detection Value Displays the current spike detection value for this channel. The value that is shown depends on the method of  spike detection used for this acquisition entity.
  1. Threshold: The spike detection value is the threshold voltage (in microvolts) used to determine if an incoming signal should be classified as a spike.  The value will look like the following when in threshold mode: 
  2. Slope:   The spike detection value is the change in voltage (in microvolts) over the change in time (milliseconds) used in calculating the slope to use for detecting spikes.  The value will look like the following when in slope mode: 
6. Clear Sub Plot Clears all data only in this waveform plot.  It does not clear any data from other waveform plots in multi-channel spike AE.
7.Spike Detection Value Up Increases the spike detection voltage value for this channel by 1 pixel.  The microvolt value of a pixel is expressed by two variables: 1) The size of the plot (i.e. making a plot larger decreases the microvolts per pixel value).  2) The input range of the channel displayed (i.e. a larger input range increases the microvolts per pixel value). The value that is adjusted depends on the method of  spike detection used for this acquisition entity.
  1. Threshold: The spike detection value is the threshold voltage used to determine if an incoming signal should be classified as a spike. 
  2. Slope:   The spike detection value is the change in voltage used in calculating the slope to use for detecting spikes.  This bar does not indicate, nor does dragging it affect, the change in time portion of the slope. 
8. Spike Detection Value Down Decreases the spike detection voltage for this channel by 1 pixel.  The microvolt value of a pixel is expressed by two variables: 1) The size of the plot (i.e. making a plot larger decreases the microvolts per pixel value).  2) The input range of the channel displayed (i.e. a larger input range increases the microvolts per pixel value). The value that is adjusted depends on the method of  spike detection used for this acquisition entity.
  1. Threshold: The spike detection value is the threshold voltage used to determine if an incoming signal should be classified as a spike. 
  2. Slope:   The spike detection value is the change in voltage used in calculating the slope to use for detecting spikes.  This bar does not indicate, nor does dragging it affect, the change in time portion of the slope. 


Feature Plot

The number of feature plots shown is configurable for each window.  You can also configure which features are plotted (see Feature Plot Properties) and which features __prod_name calculates for each acquisition entity (see -SetWaveformFeature in Spike Acquisition Entity Commands).  All values that are shown in feature plots are normalized to AD counts so that comparisons between features with disproportional values do not look skewed.

1. X Feature The name of the feature whose value corresponds to the X axis of the plot.  The name of the feature is shown along with the feature index and the channel whose feature is being shown (for single electrodes this is always 0).
2. Y Feature The name of the feature whose value corresponds to the Y axis of the plot.  The name of the feature is shown along with the feature index and the channel whose feature is being shown (for single electrodes this is always 0).
3. Quadrant 2 This quadrant represents negative X values and positive Y values.
4. Quadrant 3 This quadrant represents negative X values and negative Y values.
5. Quadrant 1 This quadrant represents positive X values and positive Y values.
6. Box Zoom Left clicking your mouse and dragging creates a green box over the feature plot.  When you stop dragging by releasing the left mouse button, the feature plot will zoom in on the section enclosed by the green box.  To return the plot to have all four quadrants visible, select All Quadrants from the view property for this plot, or by right clicking on the plot and selecting All Quadrants from the Zoom menu.
7. Quadrant 4 This quadrant represents positive X values and negative Y values.


Spike Plot Properties

The spike plot properties are shown in the properties window when a  spike window or a spike plot is selected in the properties tree. Selecting a spike window will allow you to make changes to all plots in the window.  Selecting an individual plot will only allow changes to that individual plot.

1. Plot Label Enter a label into the edit box.  The label will be displayed after the plot name in both the tree view on the properties page and in the title bar in the specified plot.
2. Plot Enable This is used when you want to stop plotting data for only a single acquisition entity's plot  in a window, but do not want to remove the plot from the window. This works like a pause button on a DVD player.  It will lock in whatever is currently displayed in the plot.  If an action is taken that will clear the plot, the last data displayed will be cleared.  No data will be added to the plot while it is disabled, but is otherwise processed normally.  

The plot enable checkbox must be in 1 of the following states:
  1. Checked :  The plot will display all data in the plot as is appropriate.
  2. Unchecked:  The will not be any new data displayed in the plot.

3.  Cluster Display Selection Controls which of the defined clusters are visible in spike plots.  See the section below for a more detailed description of the cluster display selection.
4.  Feature Plot Properties Controls the feature plot for this spike plot.  Changes will only be seen in WaveformFeature and Feature plot types or when the plot is in the maximized view.  See the section below for a more detailed description of the feature plot properties.

Feature Plot Properties

The settings for all feature plots will be adjustable from this section.  This includes the feature plots only visible when a plot is maximized.

1. Plot Number  The number of the feature plot.  The top left feature plot is plot 0, and plot numbers increase from left to right in a row, with numbering continuing at the left of the following row.
2. X Feature Select The feature whose value is represented on the X axis.   The name of the feature is shown along with the feature index and the channel whose feature is being shown (for single electrodes this is always 0).  The features available for selection can be adjusted using -SetWaveformFeature in Spike Acquisition Entity Commands)
3. Y Feature Select The feature whose value is represented on the Y axis.   The name of the feature is shown along with the feature index and the channel whose feature is being shown (for single electrodes this is always 0).  The features available for selection can be adjusted using -SetWaveformFeature in Spike Acquisition Entity Commands)
4. Feature Plot View Allows you to quickly zoom into a quadrant.  You can also change this setting by right clicking on a feature plot and selecting an option from the Zoom sub menu.  If you have zoomed into a plot via a box zoom, this will say User Defined. 


Cluster Display Selection

The selections made here affect the spikes shown in both the waveform and feature plots.  When a cell is shown, the button will be colored, if it is hidden, it will be the regular windows color.

1. Zero Cluster This will show or hide all of the spikes that are detected that do not have a cluster defined.
2. Cluster Select Buttons Clicking on the cluster number will hide or show spikes that are part of that cluster.  If there is no cluster defined for a particular number, the button will be grayed out.
3. 7+ Button Clicking on this button will hide or show all spikes that have a cluster number of 7 or greater.