Spike Sorter

Sorts spikes based on manually drawn boxes in waveform space, or boundaries in PCA space. Must be used in combination with a plugin that generates spikes, such as the Spike Detector.

Installation

This plugin can be added via the Open Ephys GUI Plugin Installer. To access the Plugin Installer, press ctrl-P or ⌘P from inside the GUI. Once the installer is loaded, browse to the "Spike Sorter" plugin and click "Install."

Important: Version 0.2.0 requires GUI v0.6.4 or higher.

Usage

Instructions for using the Spike Sorter plugin are available here.

Building from source

First, follow the instructions on this page to build the Open Ephys GUI.

Important: This plugin is intended for use with the latest version of the GUI (0.6.0 and higher). The GUI should be compiled from the main branch, rather than the former master branch.

Then, clone this repository into a directory at the same level as the plugin-GUI, e.g.:

Code
├── plugin-GUI
│   ├── Build
│   ├── Source
│   └── ...
├── OEPlugins
│   └── spike-sorter
│       ├── Build
│       ├── Source
│       └── ...

Windows

Requirements: Visual Studio and CMake

From the Build directory, enter:

cmake -G "Visual Studio 17 2022" -A x64 ..

Next, launch Visual Studio and open the OE_PLUGIN_spike-sorter.sln file that was just created. Select the appropriate configuration (Debug/Release) and build the solution.

Selecting the INSTALL project and manually building it will copy the .dll and any other required files into the GUI's plugins directory. The next time you launch the GUI from Visual Studio, the Spike Sorter plugin should be available.

Linux

Requirements: CMake

From the Build directory, enter:

cmake -G "Unix Makefiles" ..
cd Debug
make -j
make install

This will build the plugin and copy the .so file into the GUI's plugins directory. The next time you launch the compiled version of the GUI, the Spike Sorter plugin should be available.

macOS

Requirements: Xcode and CMake

From the Build directory, enter:

cmake -G "Xcode" ..

Next, launch Xcode and open the spike-sorter.xcodeproj file that now lives in the “Build” directory.

Running the ALL_BUILD scheme will compile the plugin; running the INSTALL scheme will install the .bundle file to /Users/<username>/Library/Application Support/open-ephys/plugins-api. The Spike Sorter plugin should be available the next time you launch the GUI from Xcode.

Attribution

This plugin was originally developed by Shay Ohayon in Doris Tsao's lab at Caltech. It is now being maintained by the Allen Institute.