Plugins
This section describes the configuration options of the plugins that are
included with Spyke Viewer. All included plugins create plots. They will
automatically use only the first selected object if using the whole selection
would require multiple plot windows (e.g. the signal plot plugin will only
create a plot for the first selected segment).
For information on how to create your own plugins, see
Analysis plugins.
Signal Plot
Shows the selected analog signals. A number of options enable to include
additional information in the plot.
- Use Subplots
- Determines whether multiple subplots are used or all signals are shown in
one large plot.
- Included signals
- This option can be used to tune which type of signals are shown:
AnalogSignal objects, AnalogSignalArray objects or both. In most cases, a
file will only include one of the signal types, so the default option of
including both will work well (you probably never need to change it if you
do not know the difference between the signal objects).
- Show events
- When this is checked, events in the selected trial will be shown in the
plot.
- Show epochs
- When this is checked, periods in the selected trial will be shown in the
plot.
- Show spikes
Determines whether spikes are included in the plot. The following options
are used to select from what data how the spikes are displayed:
- Display as
- Spikes can be shown as their waveform overlaid on the analog signal or a
vertical line marking their occurrence.
- Included data
- Determines whether to include spikes from SpikeTrain objects, Spike
objects, or both.
- Use first spike as template
- This option can be used for a special case: All spikes in the SpikeTrain
objects have the same waveform (e.g. because they use the same template
from spike sorting). If this option is checked, the plugin assumes that
each unit has a SpikeTrain and a single Spike. The waveform from the
Spike object is used for every spike in the SpikeTrain. The data in the
example file is structured in this way.
Spectrogram
Shows spectrograms of the selected analog signals.
- Interpolate
- Determines whether the dipslayed spectrogram is interpolated.
- Show color bar
- If this is checked, a colorbar will be shown with each plot, illustrating
the logarithmic power represented by the colors.
- FFT samples
- The number of signal samples used in each FFT window.
- Included signals
- This option can be used to tune which type of signals are shown:
AnalogSignal objects, AnalogSignalArray objects or both. In most cases, a
file will only include one of the signal types, so the default option of
including both will work well (you probably never need to change it if you
do not know the difference between the signal objects).
Correlogram
Creates auto- and crosscorrelograms for selected spike trains.
- Bin size (ms)
- The bin size used in the calculation of the correlograms.
- Cut off (ms)
- The maximum time lag for which the correlogram will be calculated and
displayed.
- Data source
The plugin supports two ways of organizing the data from which the
correlograms are created: If “Units” is selected, the spike trains for each
currently selected unit are treated as a dataset. For example, if two units
are selected, the plugin creates three subplots: one autocorrelogram for
each unit and a cross-correlogram between them.
If “Selections” are chosen, spike trains from each saved selection are
treated as a dataset. Note that the plot can only be created if all
selections contain the same number of spike trains.
- Border correction
- Determines if an automatic correction for less data at higher timelags is
applied.
Interspike Interval Histogram
Creates an interspike interval histogram for one or more units.
- Bin size (ms)
- The bin size used in the calculation of the histogram.
- Cut off (ms)
- The maximum interspike interval that is displayed.
- Type
- Determines the type of histogram. If “Bar” is selected, only the histogram
for the first selected unit is displayed. If “Line” is selected, all
selected units are included in the plot.
Peristimulus Time Histogram
Creates a peristimulus time histogram (PSTH) for one or multiple units.
- Bin size (ms)
- The bin size used in the calculation of the histogram.
- Start time (ms)
- An offset from the alignment event or start of the spike train. Calculation
of the PSTH begins at this offset. Negative values are allowed (this can be
useful when using an alignment event).
- Stop time
- A fixed stop time for calculation of the PSTH. If this is not activated,
the smallest stop time of all included spike trains is used. If the smallest
stop time is smaller than the value entered here, it will be used instead.
- Alignment event
- An event (identified by label) on which all spike trains are aligned before
the PSTH is calculated. After alignment, the event is a time 0 in the plot.
The event has to be present in all selected segments that include spike
trains for the PSTH.
- Type
- Determines the type of histogram. If “Bar” is selected, only the histogram
for the first selected unit is displayed. If “Line” is selected, all
selected units are included in the plot.
Raster Plot
Creates a raster plot from multiple spiketrains.
- Domain
- The raster plot can either be created from multiple units and one segment
(“Units”) or one unit over multiple segments (“Segments”).
- Show lines
- Determines if a small horizontal black line is displayed for each spike
train.
- Show events
- When this is checked, events in the selected trial will be shown in the
plot. If the selected domain is “Segments”, events from all selected
segments are included.
- Show epochs
- When this is checked, periods in the selected trial will be shown in the
plot. If the selected domain is “Segments”, epochs from all selected
segments are included.
Spike Density Estimation
Creates a spike density estimation (SDE) for one or multiple units. Optionally
computes the best kernel width for each unit.
- Kernel size (ms)
- The width of the kernel used for the plot. If kernel width optimization is
enabled, this parameter is not used.
- Start time (ms)
- An offset from the alignment event or start of the spike train. Calculation
of the SDE begins at this offset. Negative values are allowed (this can be
useful when using an alignment event).
- Stop time
- A fixed stop time for calculation of the SDE. If this is not activated,
the smallest stop time of all included spike trains is used. If the smallest
stop time is smaller than the value entered here, it will be used instead.
- Alignment event
- An event (identified by label) on which all spike trains are aligned before
the SDE is calculated. After alignment, the event is a time 0 in the plot.
The event has to be present in all selected segments that include spike
trains for the SDE.
- Kernel width optimization
When this option is enabled, the best kernel width for each unit is
determined using the algorithm from .
- Minimum kernel size (ms)
- The minimum kernel width that the algorithm should try.
- Maximum kernel size (ms)
- The maximum kernel width that the algorithm should try.
- Kernel size steps
- The number of steps from minimum to maximum kernel size that the algorithm
should try. The steps are distributed equidistant on a logarithmic scale.