Plugins

This page lists the plugins that come with the GUI. Most are opened from the Plugins menu. To write your own, see Extend the GUI.

Plugin	Opened from	Available in
Cluster features	Clicking a cluster in an image plot	All modes
Range controller	`Plugins → Range Controller`	All modes
3D features	`Plugins → 3D features`	All modes
Channel prediction	`Plugins → Channel Prediction`	All modes, with the `ephysatlas` extra and a session with features
Ephys features	`Plugins → Ephys Features`	`alignment-gui-ibl` only
Upload dialog	Uploading with more than one shank	All modes
QC dialog	Uploading	`alignment-gui-ibl` only

Cluster features

Shows the autocorrelogram and template waveform of a single cluster. Click a cluster in an image plot that shows cluster-level data to open a window for it.

Plugins → Cluster Features has entries to minimise or show (M) and to close (Alt+X) all the cluster windows.

Range controller

Sets the range of each plot type with a pair of sliders:

image plots and probe plots: the colour scale
line plots: the x axis

Action	How
Change a range	Drag the minimum and maximum sliders
Set an exact range	Type the value in the box beside the slider
Reset one plot type	Reset beside its sliders
Reset every plot	`R`

With more than one shank or configuration, checkboxes choose the shanks (or All) and the configurations (or both) the ranges apply to.

3D features

Shows the probe trajectory in a 3D brain.

The channels along the probe are coloured by the plot shown in the Probe plots panel, and update when it changes.
When the image plot shows clusters, the clusters are shown at their locations.

Control	Effect
Cluster marker size slider	Size of the cluster markers
Show regions	Show or hide the brain regions
Show picks	Show or hide the traced trajectory points

Channel prediction

Predicts the brain region of each channel from its electrophysiology features, and aligns the probe automatically. See Channel prediction plugin.

Ephys features

Compares the probe with other insertions in the IBL ephys atlas. Choose a brain region from those along the probe, and a feature: the feature is shown along every insertion that passes through that region, ten insertions per page, beside each insertion’s brain regions. The colour map can be changed.

Upload dialog

Shown when uploading a session with more than one shank: tick the shanks to upload, or All. The same dialog is used for Save Progress.

QC dialog

Shown in alignment-gui-ibl for each shank before its alignment is uploaded. Cancelling it cancels the upload.

Confidence of alignment: High, Medium or Low.
QC for ephys recording: Pass, Warning or Critical. For Warning or Critical, at least one problem must be ticked under Describe problem with recording. The list of problems comes from ibllib.
Resolve this alignment: Whether to mark the probe’s alignment as resolved with this alignment.
Apply to all shanks: Shown with more than one shank. Gives the remaining shanks the same assessment instead of asking for each.