thalamus-neuro 1.0.1

Data Acquisition and Behavioral Experiment Platform

Thalamus

Thalamus is an open-source Python program designed for real-time, synchronized, closed-loop multimodal data capture, specifically tailored to meet the stringent demands of neurosurgical environments.

Overview

Thalamus facilitates the advancement of clinical applications of Brain-Computer Interface (BCI) technology by integrating behavioral and electrophysiological data streams. Thalamus prioritizes the following design requirements:

1. Requires minimal setup within an operating room, clinical and research environment and could be easily controlled and quickly modified by the experimenter​
2. Operated with high reliability with few crashes​
3. Fail-safe architecture that guarantees minimal data loss in the setting of a crash​
4. Allows for real-time computation to support visualizations of research and clinical data streams​
5. Closed-loop control based on research and/or clinical data streams​
6. Acquires synchronous data from the available research and clinical sensors including relevant behavioral, physiologic, and neural sensors that could easily be scaled over time​
7. Supports a high-bandwidth, low latency, parallel distributed architecture for modular acquisition and computation that could easily be upgraded as technology continues to advance​
8. Open-source with source code available to support research use​
9. Embodies best practice in software engineering using unit tests and validation checks​
10. Supports advances in translational applications and, hence, also operates in research domains​

System Requirements

Hardware Requirements

Thalamus requires only a standard computer with enough RAM to support the in-memory operations. External hardware devices for data aquisition are dependent on the goals of individual projects.

Software Requirements

Thalamus requires Python.

OS Requirements

We provide auto builds for Linux (glibc 2.35) and Windows (10).

Python Dependencies

requirements.txt includes required dependencies if installing from Github. However, all dependencies have been packaged into the auto builds.

Installation Guide

Install from Build

Download appropriate (Windows or Linux) build directly from actions tab or under Releases.

For Windows:

python -m pip install thalamus-0.3.0-py3-none-win_amd64.whl

For Linux:

python -m pip install thalamus-0.3.0-py3-none-manylunux_2_27.whl

You should now be able to run any of the Thalamus tools

python -m thalamus.pipeline # Data pipeline, no task controller

python -m thalamus.task_controller # Data pipeline and task controller

python -m thalamus.hydrate # Convert capture files to sharable formats

Approximately 1 hour set-up time

Documentaton

The code respository for Thalamus is hosted on GitHub at https://github.com/cajigaslab/thalamus. For detailed documentation of Thalamus visit https://cajigaslab.github.io/Thalamus/. For additional examples and generation of figures in our paper, refer to the SimpleUseCase folder in the repo.

License

If you use Thalamus in your work, please remember to cite the repository in any publications.

Issues

Like all open-source projects, Thalamus will benefit from your involvement, suggestions and contributions. This platform is intended as a repository for extensions to the program based on your code contributions as well as for flagging and tracking open issues. Please use the Issues tab as fit.