Electrophysiology setup

Electrophysiology setup to use the Lead-OR platform

Requirements

1. OpenEphys: The OpenEphys GUI (v >= 0.6.4) should be installed.

2. Custom Plug-Ins: The following plug-ins should be installed to use the platform: OpenEphysIGTLink, OpenEphysLeadOR and OpenEphysRMS.

3. Data source: the OpenEphysNeuroOmega plug-in (which requires the NeuroOmega SDK; Windows only) provides an interface to use the NeuroOmega device in real-time. To test the platform, example recordings can be downloaded from here, and streamed to OpenEphys via the built-in File Readed plug-in.

Custom plug-ins installation

The links above describe the different ways to install the plug-ins. Here, only the one via GitHub CLI is described. Install GitHub CLI and run the following commands to install the plug-ins:

Windows

copy /y "C:\Program Files (x86)\AlphaOmega\Neuro Omega System SDK\CPP_SDK\win64\NeuroOmega_x64.dll" "C:\ProgramData\Open Ephys\shared-api8"
gh release download --clobber --dir "C:\ProgramData\Open Ephys\plugins-api8" --pattern *.dll --repo netstim/OpenEphysNeuroOmega
gh release download --clobber --dir "C:\ProgramData\Open Ephys\configs-api8" --pattern *.xml --repo netstim/OpenEphysNeuroOmega
gh release download --clobber --dir "C:\ProgramData\Open Ephys\plugins-api8" --pattern *.dll --repo netstim/OpenEphysRMS
gh release download --clobber --dir "C:\ProgramData\Open Ephys\shared-api8" --pattern *.dll --repo netstim/OpenEphysIGTLink
gh release download --clobber --dir "C:\ProgramData\Open Ephys\plugins-api8" --pattern *.dll --repo netstim/OpenEphysLeadOR

Building a processing pipeline

OpenEphys has a modular framework to create custom processing pipelines. Here, the default processing pipeline for Lead-OR is described. Although this example is done with example recordings, the File Reader plug-in can be replaced by the OpenEphysNeuroOmega plug-in for a novel real-time scenario.

1. Open OpenEphys GUI

2. Drag-and-drop the following plug-ins in order from the left Processors list to the Signal Chain and follow the instructions:

   1. File Reader

      • Click on F to navigate and select the downloaded example recordings.
   2. Bandpass Filter

      • Click on Channels and select all.

      • Default 300 to 6000 bandpass should be ok.

   3. LFP Viewer

   4. Root Mean Square

      • Click on Channels and select all.

      • Set window_ms to 3000.

   5. Lead-OR

      • Click on Channels and select all.

      • Check feature and set feature_name to RMS

      • See next page for the following instructions.

See following screenshot for reference:

OpenEphys signal chain.