Views

This page documents all available views in the SpikeInterface GUI, showing their functionality and appearance across different backends (desktop Qt and web panel).

Probe View

Show contact and probe shape. Units are color coded.

Controls

  • left click : select single unit

  • ctrl + left click : add unit to selection

  • mouse drag from within circle : change channel visibility and unit visibility on other views

  • mouse drag from “diamond” : change channel / unit radii size

Screenshots

Desktop (Qt)

Web (Panel)
_images/probe.png _images/probe1.png

Main settings

Overview and main controls. Can save current settings for entire GUI as the default user settings using the “Save as default settings” button.

Screenshots

Desktop (Qt)

Web (Panel)
_images/mainsettings.png _images/mainsettings1.png

Unit List

This view controls the visibility of units.

Controls

  • check box : make visible or unvisible

  • double click : make it visible alone

  • space : make selected units visible

  • arrow up/down : select next/previous unit

  • ctrl + arrow up/down : select next/previous unit and make it visible alone

  • press ‘ctrl+d’ : delete selected units (if curation=True)

  • press ‘ctrl+m’ : merge selected units (if curation=True)

  • press ‘g’ : label selected units as good (if curation=True)

  • press ‘m’ : label selected units as mua (if curation=True)

  • press ‘n’ : label selected units as noise (if curation=True)

  • drag column headers : reorder columns (Qt-only)

  • click on column header : sort by this column (Qt-only)

  • “↻” : reset the unit table

Screenshots

Desktop (Qt)

Web (Panel)
_images/unitlist.png _images/unitlist1.png

SpikeRateView View

This view shows firing rate for spikes per bin_s.

Screenshots

Desktop (Qt)

Web (Panel)
_images/spikerate.png _images/spikerate1.png

Merge View

This view allows you to compute potential merges between units based on their similarity or using the auto merge function. Select the preset to use for merging units. The available presets are inherited from spikeinterface.

Click “Calculate merges” to compute the potential merges. When finished, the table will be populated with the potential merges.

Controls

  • left click : select a potential merge group

  • arrow up/down : navigate through the potential merge groups

  • ctrl + a : accept the selected merge group

Screenshots

Desktop (Qt)

Web (Panel)
_images/merge.png _images/merge1.png

Trace View

This view shows the traces of the selected visible channels from the Probe View.

Controls

  • x size (s): Set the time window size for the traces.

  • auto scale: Automatically adjust the scale of the traces.

  • time (s): Set the time point to display traces.

  • mouse wheel: change the scale of the traces.

  • double click: select the nearest spike and center the view on it.

Screenshots

Desktop (Qt)

Web (Panel)
_images/trace.png _images/trace1.png

Trace Map View

This view shows the trace map of all the channels.

Controls

  • x size (s): Set the time window size for the traces.

  • auto scale: Automatically adjust the scale of the traces.

  • time (s): Set the time point to display traces.

  • mouse wheel: change the scale of the traces.

  • double click: select the nearest spike and center the view on it.

Screenshots

Desktop (Qt)

Web (Panel)
_images/tracemap.png _images/tracemap1.png

Waveform View

Display average template for visible units. If one spike is selected (in spike list) then the spike is super-imposed (white trace) (when the ‘plot_selected_spike’ setting is True)

There are 2 modes of display: - ‘geometry’ : snippets are displayed centered on the contact position - ‘flatten’ : snippets are concatenated in a flatten way (better to check the variance)

Controls

  • mode : change displaye mode (geometry or flatten)

  • ctrl + o : toggle overlap mode

  • ctrl + p : toggle plot waveform samples

  • mouse wheel : scale waveform amplitudes

  • alt + mouse wheel : widen/narrow x axis

  • shift + mouse wheel : zoom

  • shift + alt + mouse wheel : scale vertical spacing between channels

Screenshots

Desktop (Qt)

Web (Panel)
_images/waveform.png _images/waveform1.png

Waveform Heatmap View

Check density around the average template for each unit, which is useful to check overlap between units. For efficiency, no more than 4 units visible at same time. This can be changed in the settings.

Controls

  • mouse wheel : color range for density (important!!)

  • right click : X/Y zoom

  • left click : move

Screenshots

Desktop (Qt)

Web (Panel)
_images/waveformheatmap.png _images/waveformheatmap1.png

ISI View

This view shows the inter spike interval histograms for each unit.

Screenshots

Desktop (Qt)

Web (Panel)
_images/isi.png _images/isi1.png

Correlograms View

This view shows the auto-correlograms and cross-correlograms of the selected units.

Screenshots

Desktop (Qt)

Web (Panel)
_images/correlogram.png _images/correlogram1.png

N-dimensional Scatter View

This view projects n-dimensional principal components (num channels x num components) of the selected units in a 2D sub-space.

Controls

  • next face : rotates the projection

  • random : randomly choose a projection

  • random tour : runs dynamic “tour” of the pcs

Screenshots

Desktop (Qt)

Web (Panel)
_images/ndscatter.png _images/ndscatter1.png

Similarity View

This view displays the template similarity matrix between units.

Controls

  • left click : select a pair of units to show in the unit view.

Screenshots

Desktop (Qt)

Web (Panel)
_images/similarity.png _images/similarity1.png

Spike Amplitude View

Check amplitudes of spikes across the recording time or in a histogram comparing the distribution of ampltidues to the noise levels.

Controls

  • select : activate lasso selection to select individual spikes

  • split or ctrl+s : split the selected spikes into a new unit (only if one unit is visible)

Screenshots

Desktop (Qt)

Web (Panel)
_images/spikeamplitude.png _images/spikeamplitude1.png

Spike Depth View

Check deppth of spikes across the recording time or in a histogram.

Controls

  • select : activate lasso selection to select individual spikes

  • split or ctrl+s : split the selected spikes into a new unit (only if one unit is visible)

Screenshots

Desktop (Qt)

Web (Panel)
_images/spikedepth.png _images/spikedepth1.png

Curation View

The curation view shows the current status of the curation process and allows the user to manually visualize, revert, and export the curation data.

Controls

  • save in analyzer: Save the current curation state in the analyzer.

  • export/download JSON: Export the current curation state to a JSON file.

  • restore: Restore the selected unit from the deleted units table.

  • unmerge: Unmerge the selected merges from the merged units table.

  • submit to parent: Submit the current curation state to the parent window (for use in web applications).

  • press ‘ctrl+r’: Restore the selected units from the deleted units table.

  • press ‘ctrl+u’: Unmerge the selected merges from the merged units table.

  • press ‘ctrl+x’: Unsplit the selected split groups from the split units table.

Screenshots

Desktop (Qt)

Web (Panel)
_images/curation.png _images/curation1.png

Metrics View

View and explore unit metrics in a customizable grid of plots.

Screenshots

Desktop (Qt)

Web (Panel)
_images/metrics.png _images/metrics1.png

Spike list View

Show all spikes of the visible units. When spikes are selected, they are highlighted in the Spike Amplitude View and the ND SCatter View. When a single spike is selected, the Trace and TraceMap Views are centered on it.

Controls

  • ↻ spikes: refresh the spike list

  • clear: clear the selected spikes

  • shift + arrow up/down : select next/previous spike and make it visible alone

Screenshots

Desktop (Qt)

Web (Panel)
_images/spikelist.png _images/spikelist1.png

Amplitude Scalings View

Amplitude scalings measure the optimal scaling which should be applied to the template so that it best matches each spike waveform.

Controls

  • select : activate lasso selection to select individual spikes

  • split or ctrl+s : split the selected spikes into a new unit (only if one unit is visible)

Screenshots not available for this view.

Main Template View

Display average template on main channel. If the template_metrics are computed, it also displayed the template signal used to compute metrics (usually upsampled) and the trough/peak_before/peak_after positions and widths.

  • troughs are negative extrema and are displayed with a downward triangle symbol

  • peaks are positive extrema and are displayed with an upward triangle symbol

Screenshots

Desktop (Qt)

Web (Panel)
_images/maintemplate.png _images/maintemplate1.png