Plugins

The IBL Alignment GUI supports a plugin architecture that allows users to extend the GUI with additional functionality. Plugins can be used to add new visualizations, interactive tools, or auxiliary views that integrate with the main GUI.

This section describes the currently available plugins and how to use them. The Channel Prediction plugin, which predicts the brain region of each channel from its electrophysiology features, has its own page: see Channel Prediction.

Cluster Plugin

The Cluster plugin allows users to inspect individual spike-sorted clusters by visualizing their waveforms and inter-spike interval (ISI) distributions.

The plugin is attached to image plots that display cluster-level data.

Usage

To use the Cluster plugin:

  1. Ensure an image plot displaying cluster-level data is active

  2. Click on an individual cluster in the image plot

A new window will open showing:

  • The waveform of the selected cluster

  • The ISI distribution for that cluster

Keyboard Shortcuts

Shortcut

Action

M

Minimise / show the plugin windows

Alt+X

Close the plugin windows

Range Controller

The Range Controller plugin allows users to interactively adjust the data range displayed in different plot types.

The effect of the range controller depends on the plot type:

  • Image plots and probe plots: Adjusts the color scale range

  • Line plots: Adjusts the x-axis range

Usage

The Range Controller can be launched from the Plugins menu bar.

When opened, a new window appears with sliders controlling the minimum and maximum range values for each plot type.

When working with multi-shank or dual-configuration data, a radio button selector allows you to choose which shank or configuration the range controls apply to.

Adjusting Ranges

Action

Method

Adjust range

Drag the min/max sliders for the desired plot type

Set an exact range

Type the value into the box beside the corresponding slider

Reset single plot range

Click Reset button next to the corresponding slider

Reset all plot ranges

Press R

3D Brain Viewer

The 3D Brain Viewer plugin provides a three-dimensional visualization of the probe trajectory within a brain model.

Usage

Launch the 3D Brain Viewer from the Plugins menu bar.

A new window will open displaying:

  • A 3D brain model

  • The probe trajectory overlaid in 3D space

The feature data shown along the probe automatically updates as you change the probe plots in the main GUI.

If a cluster plot is selected in the image plot, the corresponding cluster locations will be displayed in the 3D brain viewer.

Display Controls

Control

Function

Cluster marker size slider

Adjust size of cluster markers

Show regions checkbox

Show / hide anatomical brain regions

Show picks checkbox

Show / hide probe trajectory picks

Adding Additional Plots

Custom plots can be added to the GUI via the plugin system, without modifying the GUI itself.

ibl_alignment_gui/plugins/allen/additional_plots_allen.py is a worked example. It shows how a plugin adds its own plots by attaching new plot methods to the plot loader, so that they appear in the menu bars alongside the built-in plots. ibl_alignment_gui/plugins/allen/custom_filters.py does the same for the unit filters, adding new entries to the Filter Plots menu.

Note

Detailed developer documentation for writing custom plugins and additional plots will be provided in a future release.