ONIX: An Open-Source Platform for Multimodal Neural Recording and Perturbation During Naturalistic Behavior

Research Background and Significance

In recent years, significant advances have been made in large-scale neural population recording technology and studies on animal behavior in the field of neuroscience. However, these two demands often conflict. To obtain high-quality neural data, many studies use head-fixed experimental methods, which limit the natural behavior of animals. Increasingly, studies have shown that neural activity during natural behaviors differs significantly from that observed in fixed experimental conditions. For example, motor behavior can influence the activity of brain areas previously believed to be primarily sensory-focused, and learning strategies differ noticeably between fixed and free-moving conditions. These findings highlight the necessity of conducting neural recordings in the context of natural behavior to study complex neural functions such as social interactions, learning, and cognition.

Traditional recording methods often employ bulky equipment and cables, which not only restrict animal movement but also make long-term recording or experiments in large spaces challenging. This is particularly problematic for small experimental animals (e.g., mice). Therefore, designing a lightweight, high-efficiency data acquisition system that can achieve long-term neural data recording while maintaining freedom of behavior is critically important for advancing neuroscience research.

To address this challenge, scientists from multiple research institutions, including the Massachusetts Institute of Technology (MIT), Allen Institute, and HHMI Janelia Research Campus, have jointly developed a platform called ONIX. This open-source data acquisition system enables neural recording and perturbation under conditions of naturalistic behavior.

Source of the Paper

This research was conducted by scientists Jonathan P. Newman, Jie Zhang, Nicholas J. Miller, and others, representing institutions such as the Department of Brain and Cognitive Sciences at MIT, Picower Institute for Learning and Memory, and McGovern Institute for Brain Research at MIT. The paper was published in the January 2025 issue of Nature Methods (Volume 22, pp. 187–192), DOI: 10.1038/s41592-024-02521-1.

Research Workflow

The paper introduces the design, technical features, and experimental validation process of ONIX. The research workflow can be broken down into the following steps:

1. Design and Development of the ONIX System

The core of the ONIX system is an open-source, modular, and extensible platform aimed at reducing the impact of neural recording on free behavior. The system’s primary architecture includes the following modules: - Hardware Standards and Interfaces: Utilizes an open hardware standard (Open Neuro Interface, ONI) and API (Application Programming Interface) to support communication and data synchronization across multiple devices. - Micro-Coaxial Cable (micro-coax tether): With a diameter of only 0.31 mm and a weight of approximately 0.37 g per meter, it significantly reduces the torque exerted on the animal’s head compared to traditional cables with a 3-mm diameter, greatly minimizing behavioral interference. - Motorized Commutator: Integrates a nine-axis sensor to calculate the animal’s head rotation in real time and uses a small motor to eliminate cable twisting without the need for additional torque measurements.

2. System Compatibility and Hardware Configuration

ONIX supports multiple data acquisition devices, including: - Neural Electrodes (tetrode drives) and Neuropixels probes: Used for passive electrical recordings and high-density neural recordings, respectively. - Head-Mounted Microscopes: Such as UCLA Miniscopes. - Cameras and 3D Tracking Sensors: Capture real-time movement positions and head postures of animals in three dimensions.

In the experiments, ONIX also integrated various sensors and actuators, such as optical stimulators, nine-axis Inertial Measurement Units (IMUs), and LED/laser diode drivers.

3. Behavioral and Neural Experimental Validation

a) Long-Duration Experiments

The research team first conducted an 8-hour long-duration recording of freely moving mice using ONIX. The experimental setting was a 1.5 m × 1.5 m × 0.5 m hexagonal three-dimensional arena with foam modules of varying heights, allowing mice to perform natural behaviors such as running, climbing, and jumping.

By comparing the lightweight ONIX cable with traditional cables, the mice exhibited significantly increased exploratory behavior when using ONIX. The spatial trajectory distribution and head orientation entropy values closely resembled those of non-implanted mice.

b) Mapping Natural Behavior to Neural Activity

ONIX enabled scientists to record neural activity before and after unique behaviors (e.g., jumping). For example, specific neural activity patterns were observed in the cortex during jumping behavior. Furthermore, tests showed no significant brain displacement during high-speed motion or jumps.

c) Multi-Day Sleep Recordings

To verify the long-term stability of ONIX, the research team conducted a 55-hour continuous experiment in a large cage environment, including neural activity recordings across different sleep phases. The experiment demonstrated that the system could reliably capture tangle-free data for extended periods.

4. Data Integration and Visualization

With its open API design, ONIX allowed the research team to synchronize and integrate multiple data sources using open-source software such as Bonsai. Additionally, the use of real-time deep learning behavior tracking tools (e.g., DeepLabCut and SLEAP) validated ONIX’s functional compatibility, enabling highly precise dynamics of neural-behavior interactions.

Research Results and Significance

Through a series of experiments, the researchers demonstrated ONIX’s ability to capture high-quality neural data during naturalistic behavior over long durations. The main findings are as follows: 1. Neural Recording Under Natural Behavior: ONIX enables extended-duration recording without interfering with free behavior, which is extremely rare in existing systems. 2. Zero-Torque Design for Head Rotation: Under identical experimental conditions, ONIX significantly reduced the impact of high torque on the freedom of animal behavior compared to traditional systems. 3. Compatibility with Probes and Hardware Extensibility: The ONIX system supports multiple device integration interfaces and is compatible with widely used Neuropixels probes, Miniscopes, and multiple camera modules.

Importance and Value of the Research

The development of ONIX represents a breakthrough in neuroscience: 1. Scientific Value: The research emphasizes the importance of naturalistic behavior in experimental neuroscience design. This will greatly enhance our understanding of fields such as social behavior, learning, and cognition. 2. Applied Value: ONIX provides a universal hardware platform that enables scientists to develop highly flexible and precise neural-behavior experiments. 3. A Milestone in Open-Source Research Tools: The fully open-source design of ONIX not only promotes global collaboration but also significantly lowers the barrier for laboratories to create customized scientific instruments.

In conclusion, this study introduces a revolutionary research tool that fills a technical gap in large-scale neural recordings in natural environments, providing crucial support for innovative research in biological and cognitive sciences.