Software Guide

There are two recommended software programs to acquire data from the ONIX system. Click on the cards below to navigate to their respective documentation sites.

Bonsai Package OpenEphys.Onix1

Acquire data from ONIX in Bonsai, a visual programming language for more extensive data processing and sub-ms latency feedback.

https://open-ephys.github.io/bonsai-onix1-docs/

Open Ephys GUI Plugin ONIX Source

Acquire data from ONIX in the Open Ephys GUI, a turnkey solution for acquiring and visualizing electrophysiology data.

https://open-ephys.github.io/gui-docs/User-Manual/Plugins/Onix-Source.html

Both platforms are free, open-source, and widely adopted in the neuroscience community. There are a few important considerations when selecting which to use, which you can read about below.

Software Comparison

User Experience

Open Ephys GUI is a user-friendly application specialized for acquiring, processing, and visualizing electrophysiology data by connecting processors to form signal chains. Bonsai is a visual programming language for acquiring, processing, and visualizing a variety of data types by connecting nodes/operators to form workflows. The Open Ephys GUI is typically easier for beginners, while Bonsai rewards expertise with greater flexibility such as being able to apply complex logic to asynchronous data streams for the purpose of coordinating behavioral experiments and/or stimulus delivery.

3rd Party Hardware and Software Support

The Open Ephys GUI natively supports various neural data acquisition systems (see the User Manual introduction page) as well as a few other 3rd party devices (view the list of plugins in the table of contents). Bonsai offers a larger array of 3rd party hardware options. Some families of devices that are supported in Bonsai and not in the Open Ephys GUI include cameras, miniscopes, Harp, and more. Additionally, Bonsai is capable of integrating SLEAP and DeepLabCut for pose estimation or BonVision for the presentation of virtual environments or visual stimuli. The Open Ephys GUI does not have video capabities.

Example signal chain in the Open Ephys GUI

Example workflow in Bonsai

ONIX Support

The OpenEphys.Onix1 package in Bonsai supports the full set ONIX’s features. The ONIX Source plugin in the Open Ephys GUI supports a subset. For more details, visit the ONIX Source plugin page.

Performance/Closed-Loop Latency

The Open Ephys GUI operates on the order of 20ms closed-loop latencies. Bonsai is capable of operating on the order of sub-millisecond closed-loop latencies and with lower variability of latencies.

Data Visualization

The Open Ephys GUI provides visualization tools specialized for presenting electrophysiology voltage data such as the LFP viewer with different waveform and raster views, and the Probe viewer for displaying high-density probe data. Bonsai provides type visualizers which are more agnostic to the kind of data that is being streamed.

LFP Viewer in the Open Ephys GUI

Type visualizer in Bonsai

Visualization of ephys data in Bonsai is undergoing improvement with the integration of Dear ImGUI in the Bonsai.Ephys package. Also, Open Ephys GUI visualization tools can be used to visualize data acquired from Bonsai using sockets, as explained in this tutorial.

Neuropixels Open Ephys GUI visualizer used for data acquired in Bonsai

ImGUI visualizer in Bonsai

Extensibility

Both options are open-source and provide options for extending functionality by providing the capability for users to create custom processors in the Open Ephys GUI or custom operators and packages in Bonsai. Both can also stream data to external applications using sockets. Bonsai additionally provides packages for including Python code in Bonsai workflows.

Troubleshooting & Development

oni_repl is a simple command-line application that can be used for debugging and basic streaming IO with ONIX hardware.

Tip

ONIX uses an ONI-compliant API that is software agnostic. If you want to use ONIX hardware with your acquisition software, please get in touch.

Deprecated Software

Bonsai.ONIX is the deprecated Bonsai ONIX package which has been superseded by OpenEphys.Onix1.