Menus

This page lists every entry in the menu bar. The plot menus list only the plots for which data was found, so some entries appear only with certain datasets or modes. Hover over a greyed-out menu to see why it is unavailable.

Image Plots

One plot at a time, in the left panel of the Ephys figure. Alt+1 / Shift+Alt+1 cycle through them.

Entry	Shows	Needs
`Amplitude`	Every spike by time and depth, coloured by amplitude	Spike sorting
`Cluster Amp vs Depth vs FR`	Clusters by amplitude and depth, coloured by firing rate	Spike sorting
`Cluster Amp vs Depth vs Duration`	Clusters by amplitude and depth, coloured by peak-to-trough duration	Spike sorting
`Cluster FR vs Depth vs Amp`	Clusters by firing rate and depth, coloured by amplitude	Spike sorting
`Firing Rate`	Firing rate over time and depth	Spike sorting
`Correlation`	Correlation of activity between depths	Spike sorting
`rms AP`	AP band RMS over time and depth	`_iblqc_ephysTimeRmsAP`
`rms LF`	LF band RMS over time and depth	`_iblqc_ephysTimeRmsLF`
`LF spectrum`	LF power by frequency and depth	`_iblqc_ephysSpectralDensityLF`
`Raw ap snippet <n>`, `Raw lf snippet <n>`	Short snippets of the raw data	Raw AP or LF data

Clicking a cluster in a cluster plot opens its waveform (see Plugins).

Line Plots

Entry	Shows	Needs
`Firing Rate`	Mean firing rate along depth	Spike sorting
`Amplitude`	Mean amplitude along depth	Spike sorting
`Dead Channels`	Channels detected as dead	Raw AP data
`Noisy Channels Coherence`	Channels detected as noisy by coherence	Raw AP data
`Noisy Channels PSD`	Channels detected as noisy by power spectrum	Raw AP data
`Outside Channels`	Channels detected as outside the brain	Raw AP data

Alt+2 / Shift+Alt+2 cycle through them.

Probe Plots

Drawn on the probe geometry. The channels in the Slice figure are coloured by the plot shown here. Alt+3 / Shift+Alt+3 cycle through them.

Entry	Shows	Needs
`rms AP`, `rms LF`	Mean RMS per channel	`_iblqc_ephysTimeRms*`
`0 - 4 Hz`, `4 - 10 Hz`, `10 - 30 Hz`, `30 - 80 Hz`, `80 - 200 Hz`	LF power per channel in each band	`_iblqc_ephysSpectralDensityLF`
`Ephys Atlas - <feature>`	One ephys-atlas feature per channel	The `ephysatlas` extra and a features file

Feature Plots

Only shown with the ephysatlas extra. Greyed out when the session has no ephys-atlas features.

Entry	Shows	Needs
`Ephys Atlas`	Every ephys-atlas feature side by side	The `ephysatlas` extra and a features file

Slice Plots

The image in the Slice figure. Alt+4 / Shift+Alt+4 cycle through them.

Entry	Shows
`CCF`	Allen atlas average template
`Annotation`	Allen atlas annotation
`Histology red`, `Histology green`	Your histology volumes, when given (see Input datasets)

Prediction Plots

The predictions of the channel prediction models, in a panel beside the ephys plots. Alt+5 / Shift+Alt+5 cycle through them. Only shown with the ephysatlas extra. Greyed out when the session has no ephys-atlas features.

Entry	Shows
`None`	No prediction panel
Model entries	Predicted regions and auto-alignment (see Channel prediction plugin)
`All predictions (side by side)`	Every prediction, side by side, instead of the image, line and probe plots (`Shift`+`P`)

Set Mapping

The atlas mapping of the brain regions in the Histology figure. Alt+M / Shift+Alt+M cycle through them.

Entry	Shows
`Allen`, `Beryl`, `Cosmos`	Atlas regions at three levels of detail (see Brain region mappings)

Filter Plots

The units shown in the spike sorting plots. Greyed out when the session has no spike sorting.

Entry	Units shown
`All`	Every unit
`KS good`	kilosort good units (`ks2_label`)
`KS mua`	kilosort multi-unit (`ks2_label`)
`IBL good`	Units passing the IBL metrics (`label`)
Custom filters	Added by plugins (see How to add your own unit filter)

Fit Options

Entry	Shortcut
`Fit`	`Enter`
`Remove Line`	`Shift`+`D`
`Next`	`Shift`+`Right`
`Previous`	`Shift`+`Left`
`Reset`	`Shift`+`R`
`Upload`	`Shift`+`U`
`Save Progress`	`Shift`+`S`

Display Options

Entry	Shortcut
`Toggle Image Plots ->` … `Toggle Prediction Plots ->`	`Alt`+`1` … `Alt`+`5`
`Toggle Image Plots <-` … `Toggle Prediction Plots <-`	`Shift`+`Alt`+`1` … `Shift`+`Alt`+`5`
`Toggle Mapping ->` / `Toggle Mapping <-`	`Alt`+`M` / `Shift`+`Alt`+`M`
`Reset Axis`	`Shift`+`A`
`Hide/Show Labels`	`Shift`+`L`
`Hide/Show Lines`	`Shift`+`H`
`Hide/Show Channels`	`Shift`+`C`
`Toggle layout`	`T`
`All Predictions`	`Shift`+`P`
`Next shank`	`Right`
`Previous shank`	`Left`
`Reset Range`	`R`

Plugins

Entry	See
`Cluster Features`	Minimise or close the cluster windows
`Range Controller`	Plugins
`3D features`	Plugins
`Channel Prediction`	Channel prediction plugin
`Ephys Features`	Plugins (`alignment-gui-ibl` only)