tne-lab / coherence-viewer

Real-time coherence visualization for the Open Ephys GUI

Coherence Viewer

This plugin for the Open Ephys GUI preforms real time coherence estimation between two groups of channels. The primary purpose of this plugin is to visualize the coherence between two brain regions in real time to get feedback on the effects of a stimulus - electrical/opto stimulation, task or environmental changes, etc. The plugin allows the user to choose channels to correspond to two different groups. Each channel combination between the two groups will be analyzed. Individual combinations or the average across all combinations can be chosen as the visualization. See video.

Installation

This plugin must now be built outside of the main GUI file tree using CMake. In order to do so, it must be in a sibling directory to plugin-GUI\ and the main GUI must have already been compiled using cmake. The coherence-viewer folder should be the sibling directory.

You must also first install the "OpenEphysFFTW" common library, available here. You must build the install project in the solution.

See CoherenceViewer/CMAKE_README.txt and/or the wiki page here for build instructions.

If you have the GUI built somewhere else, you can specify its location by setting the environment variable GUI_BASE_DIR or defining it when calling cmake with the option -DGUI_BASE_DIR=<location>.

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Usage

1. Choose channels in G1/G2 Chans to be split into groups. Default is first half of channels in G1 and second half in G2.

2. Choose whether to have a linear or exponential running average of the coherence.

   Exponential determined by equation ...

3. Set a microvolt threshold for artifact detection. The plugin will discard buffers with an artifact. A pop up will appear after the first discarded buffer to warn users that not all information is used.

4. Set you frequencies of interest. Click the Reset button to set up the plugin.

5. Start acquisition!

   * If recording a second experiment, click reset again to flush buffers and reset coherence.

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If recording. The coherence output after each window will be saved in recording directory. This is still in an experimental form and will be improved on in the future.

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Development

Note this plugin is still in active development. There are still bugs to be found and functions to be implemented! Contact [email protected] with any ideas!

coherence-viewer's Issues

Releasing via Plugin Installer

Hello! The Open Ephys development team would like to make this plugin available to the community via the GUI's Plugin Installer.

Before we do that, we have a few questions:

• Is the code on GitHub up to date?
• Are there any particular features that need improvement? We are happy to put some effort in to make the plugin as general-purpose as possible
• Is there additional documentation available beside what's in the README file? We will be adding a page dedicated to this plugin on the GUI's new docs site.
• Is there a sample dataset you've been using for testing/benchmarking?

Thanks!