An embedded system for real-time feedback neuroscience experiments

• Published in: arXiv.org 2015-04
• Main Authors: Lirio Onofre Baptista de Almeida, Matias, Paulo, Rafael Tuma Guariento
• Format: Article
• Language: English
• Subjects: Brain; Chemical activity; Closed loops; Co-design; Commercial off-the-shelf technology; Data storage; Electric bridges; Embedded systems; Experiments; Graphical user interface; Hardware; HyperText Markup Language; In vivo methods and tests; Man-machine interfaces; Microprocessors; Mobile communication systems; Neurons; Neurosciences; Organic chemistry; Real time; Spikes; Stimuli
• ISSN: 2331-8422
• DOI: 10.48550/arxiv.1504.00932

A complete data acquisition and signal output control system for synchronous stimuli generation, geared towards in vivo neuroscience experiments, was developed using the Terasic DE2i-150 board. All emotions and thoughts are an emergent property of the chemical and electrical activity of neurons. Most of these cells are regarded as excitable cells (spiking neurons), which produce temporally localized electric patterns (spikes). Researchers usually consider that only the instant of occurrence (timestamp) of these spikes encodes information. Registering neural activity evoked by stimuli demands timing determinism and data storage capabilities that cannot be met without dedicated hardware and a hard real-time operational system (RTOS). Indeed, research in neuroscience usually requires dedicated electronic instrumentation for studies in neural coding, brain machine interfaces and closed loop in vivo or in vitro experiments. We developed a complete embedded system solution consisting of a hardware/software co-design with the Intel Atom processor running a free RTOS and a FPGA communicating via a PCIe-to-Avalon bridge. Our system is capable of registering input event timestamps with 1{\mu}s precision and digitally generating stimuli output in hard real-time. The whole system is controlled by a Linux-based Graphical User Interface (GUI). Collected results are simultaneously saved in a local file and broadcasted wirelessly to mobile device web-browsers in an user-friendly graphic format, enhanced by HTML5 technology. The developed system is low-cost and highly configurable, enabling various neuroscience experimental setups, while the commercial off-the-shelf systems have low availability and are less flexible to adapt to specific experimental configurations.