RTHybrid: a standardized and open-source real-time software model library for experimental neuroscience

ABSTRACTClosed-loop technologies provide novel ways of online observation, control and bidirectional interaction with the nervous system, which help to study complex non-linear and partially observable neural dynamics. These protocols are often difficult to implement due to the temporal precision required when interacting with biological components, which in many cases can only be achieved using real-time technology. In this paper we introduce RTHybrid (www.github.com/GNB-UAM/RTHybrid), a free and open-source software that includes a neuron and synapse model library to build hybrid circuits with living neurons in a wide variety of experimental contexts. In an effort to encourage the standardization of real-time software technology in neuroscience research, we compared different open-source real-time operating system patches, RTAI, Xenomai 3 and Preempt-RT, according to their performance and usability. RTHybrid has been developed to run over Linux operating systems supporting both Xenomai 3 and Preempt-RT real-time patches, and thus allowing an easy implementation in any laboratory. We report a set of validation tests and latency benchmarks for the construction of hybrid circuits using this library. With this work we want to promote the dissemination of standardized, user-friendly and open-source software tools developed for open- and closed-loop experimental neuroscience.

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BonVision – an open-source software to create and control visual environments

10.1101/2020.03.09.983775 ◽

2020 ◽

Cited By ~ 4

Author(s):

Gonçalo Lopes ◽

Karolina Farrell ◽

Edward A. B. Horrocks ◽

Chi-Yu Lee ◽

Mai M. Morimoto ◽

...

Keyword(s):

Open Source ◽

Real Time ◽

Open Source Software ◽

Brain Function ◽

Deep Neural Networks ◽

Closed Loop ◽

Physiological Measurement ◽

Graphical Programming ◽

Time Interaction ◽

And Control

Real-time rendering of closed-loop visual environments is necessary for next-generation understanding of brain function and behaviour, but is prohibitively difficult for non-experts to implement and is limited to few laboratories worldwide. We developed BonVision as an easy-to-use open-source software for the display of virtual or augmented reality, as well as standard visual stimuli. As the architecture is based on the open-source Bonsai graphical programming language, BonVision benefits from native integration with experimental hardware. BonVision therefore enables easy implementation of closed-loop experiments, including real-time interaction with deep neural networks and communication with behavioural and physiological measurement and manipulation devices.

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Creating and controlling visual environments using BonVision

eLife ◽

10.7554/elife.65541 ◽

2021 ◽

Vol 10 ◽

Author(s):

Gonçalo Lopes ◽

Karolina Farrell ◽

Edward A B Horrocks ◽

Chi Yu Lee ◽

Mai M Morimoto ◽

...

Keyword(s):

Open Source ◽

Real Time ◽

Open Source Software ◽

Brain Function ◽

Deep Neural Networks ◽

Closed Loop ◽

Experimental Designs ◽

Physiological Measurement ◽

Graphical Programming ◽

Time Interaction

Real-time rendering of closed-loop visual environments is important for next-generation understanding of brain function and behaviour, but is often prohibitively difficult for non-experts to implement and is limited to few laboratories worldwide. We developed BonVision as an easy-to-use open-source software for the display of virtual or augmented reality, as well as standard visual stimuli. BonVision has been tested on humans and mice, and is capable of supporting new experimental designs in other animal models of vision. As the architecture is based on the open-source Bonsai graphical programming language, BonVision benefits from native integration with experimental hardware. BonVision therefore enables easy implementation of closed-loop experiments, including real-time interaction with deep neural networks, and communication with behavioural and physiological measurement and manipulation devices.

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RTHybrid: A Standardized and Open-Source Real-Time Software Model Library for Experimental Neuroscience

Frontiers in Neuroinformatics ◽

10.3389/fninf.2019.00011 ◽

2019 ◽

Vol 13 ◽

Cited By ~ 2

Author(s):

Rodrigo Amaducci ◽

Manuel Reyes-Sanchez ◽

Irene Elices ◽

Francisco B. Rodriguez ◽

Pablo Varona

Keyword(s):

Open Source ◽

Real Time ◽

Model Library ◽

Software Model

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Powering Real-time Decision Engines in Finance and Healthcare using Open Source Software

Proceedings of the 21th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining - KDD '15 ◽

10.1145/2783258.2790457 ◽

2015 ◽

Author(s):

Bassel Ojjeh

Keyword(s):

Open Source ◽

Real Time ◽

Open Source Software

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Prospects of Open Source Software for Maximizing the User Expectations in Heterogeneous Network

Research Anthology on Usage and Development of Open Source Software ◽

10.4018/978-1-7998-9158-1.ch014 ◽

2021 ◽

pp. 257-271

Author(s):

Pushpa Singh ◽

Rajeev Agrawal

Keyword(s):

Machine Learning ◽

Open Source ◽

Real Time ◽

Open Source Software ◽

Heterogeneous Networks ◽

Heterogeneous Network ◽

Research Work ◽

Software Tool ◽

Knn Classifier ◽

User Expectations

This article focuses on the prospects of open source software and tools for maximizing the user expectations in heterogeneous networks. The open source software Python is used as a software tool in this research work for implementing machine learning technique for the categorization of the types of user in a heterogeneous network (HN). The KNN classifier available in Python defines the type of user category in real time to predict the available users in a particular category for maximizing profit for a business organization.

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Development of an All-Fiber Coherent Doppler Lidar in the IAO SB RAS

EPJ Web of Conferences ◽

10.1051/epjconf/202023706005 ◽

2020 ◽

Vol 237 ◽

pp. 06005

Author(s):

Artem Sherstobitov ◽

Viktor Banakh ◽

Alexander Nadeev ◽

Igor Razenkov ◽

Igor Smalikho ◽

...

Keyword(s):

Signal Processing ◽

Radial Velocity ◽

Open Source ◽

Real Time ◽

Open Source Software ◽

Stream Line ◽

Doppler Lidar ◽

Hardware System ◽

Coherent Doppler Lidar

Paper presents a model of the all-fiber pulsed coherent Doppler lidar (IAO-lidar) build in the IAO SB RAS. Here is described lidar design, the algorithm for processing of lidar signals and the software-hardware system that implements signal processing in real time, created with the use of open source software. The results of joint measurements of the radial velocity by the IAO-lidar and the HALO Photonics (Stream Line) lidar are given.

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Embedded Real-Time Linux for Cable Robot Control

Volume 1: 22nd Computers and Information in Engineering Conference ◽

10.1115/detc2002/cie-34506 ◽

2002 ◽

Cited By ~ 4

Author(s):

Frederick M. Proctor ◽

William P. Shackleford

Keyword(s):

Open Source ◽

Real Time ◽

Open Source Software ◽

Hard Disk Drives ◽

Source Model ◽

Disk Drives ◽

Deterministic Scheduling ◽

Cable Robot ◽

Real Time Computing ◽

Embedded Applications

Linux is a version of the Unix operating system distributed according to the open source model. Programmers are free to adapt the source code for their purposes, but are required to make their modifications or enhancements available as open source software as well. This model has fostered the widespread adoption of Linux for typical Unix server and workstation roles, and also in more arcane applications such as embedded or real-time computing. Embedded applications typically run in small physical and computing footprints, usually without fragile peripherals like hard disk drives. Special configurations are required to support these limited environments. Real-time applications require guarantees that tasks will execute within their deadlines, something not possible in general with the normal Linux scheduler. Real-time extensions to Linux enable deterministic scheduling, at task periods at tens of microseconds. This paper describes embedded and real-time Linux, and an application for distributed control of a Stewart Platform cable robot. Special Linux configuration requirements are detailed, and the architecture for teleoperated control of the cable robot is presented, with emphasis on the resolved-rate control of the suspended platform.

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Real-time traffic-based routing, based on open data and open-source software

2016 IEEE 3rd World Forum on Internet of Things (WF-IoT) ◽

10.1109/wf-iot.2016.7845419 ◽

2016 ◽

Cited By ~ 4

Author(s):

Diego Serrano ◽

Teresa Baldassarre ◽

Eleni Stroulia

Keyword(s):

Open Source ◽

Real Time ◽

Open Source Software ◽

Open Data ◽

Real Time Traffic

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Prediction of the Testing Effort for the Safety Certification of Open-Source Software: A Case Study on a Real-Time Operating System

2016 12th European Dependable Computing Conference (EDCC) ◽

10.1109/edcc.2016.22 ◽

2016 ◽

Cited By ~ 2

Author(s):

Domenico Cotroneo ◽

Domenico Di Leo ◽

Roberto Natella ◽

Roberto Pietrantuono

Keyword(s):

Operating System ◽

Open Source ◽

Real Time ◽

Open Source Software ◽

Real Time Operating System ◽

Testing Effort ◽

Safety Certification

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Open source modules for tracking animal behavior and closed-loop stimulation based on Open Ephys and Bonsai

10.1101/340141 ◽

2018 ◽

Cited By ~ 1

Author(s):

Alessio Paolo Buccino ◽

Mikkel Elle Lepperød ◽

Svenn-Arne Dragly ◽

Philipp Häfliger ◽

Marianne Fyhn ◽

...

Keyword(s):

Open Source ◽

Real Time ◽

Closed Loop ◽

Low Cost ◽

Data Formats ◽

Behavioral Tracking ◽

Real Time Tracking ◽

Set Up ◽

And Behavior ◽

Closed Loop Stimulation

AbstractObjectiveA major goal in systems neuroscience is to determine the causal relationship between neural activity and behavior. To this end, methods that combine monitoring neural activity, behavioral tracking, and targeted manipulation of neurons in closed-loop are powerful tools. However, commercial systems that allow these types of experiments are usually expensive and rely on non-standardized data formats and proprietary software which may hinder user-modifications for specific needs. In order to promote reproducibility and data-sharing in science, transparent software and standardized data formats are an advantage. Here, we present an open source, low-cost, adaptable, and easy to set-up system for combined behavioral tracking, electrophysiology and closed-loop stimulation.ApproachBased on the Open Ephys system (www.open-ephys.org) we developed multiple modules to include real-time tracking and behavior-based closed-loop stimulation. We describe the equipment and provide a step-by-step guide to set up the system. Combining the open source software Bonsai (bonsai-rx.org) for analyzing camera images in real time with the newly developed modules in Open Ephys, we acquire position information, visualize tracking, and perform tracking-based closed-loop stimulation experiments. To analyze the acquired data we provide an open source file reading package in Python.Main resultsThe system robustly visualizes real-time tracking and reliably recovers tracking information recorded from a range of sampling frequencies (30-1000Hz). We combined electrophysiology with the newly-developed tracking modules in Open Ephys to record place cell and grid cell activity in the hippocampus and in the medial entorhinal cortex, respectively. Moreover, we present a case in which we used the system for closed-loop optogenetic stimulation of entorhinal grid cells.SignificanceExpanding the Open Ephys system to include animal tracking and behavior-based closed-loop stimulation extends the availability of high-quality, low-cost experimental setup within standardized data formats serving the neuroscience community.

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