Creating and controlling visual environments using BonVision

Abstract

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.

Data availability

BonVision is an open-source software package available to use under the MIT license. It can be downloaded through the Bonsai (bonsai-rx.org) package manager, and the source code is available at: github.com/bonvision/BonVision. All benchmark programs and data are available at https://github.com/bonvision/benchmarks. Installation instructions, demos and learning tools are available at: bonvision.github.io/.

Article and author information

Author details

  1. Gonçalo Lopes

    NeuroGears, London, United Kingdom
    Competing interests
    Gonçalo Lopes, Gonçalo Lopes is affiliated with NeuroGEARS Ltd. The author has no financial interests to declare..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0731-4945
  2. Karolina Farrell

    Experimental Psychology, University College London, London, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0707-2838
  3. Edward A B Horrocks

    Experimental Psychology, University College London, London, United Kingdom
    Competing interests
    No competing interests declared.
  4. Chi Yu Lee

    Experimental Psychology, University College London, London, United Kingdom
    Competing interests
    No competing interests declared.
  5. Mai M Morimoto

    Department of Experimental Psychology, University College London, London, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9654-3960
  6. Tomaso Muzzu

    Institute of Behavioural Neuroscience, University College London, London, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0018-8416
  7. Amalia Papanikolaou

    Institute of Behavioural Neuroscience, University College London, London, United Kingdom
    Competing interests
    No competing interests declared.
  8. Fabio R Rodrigues

    Experimental Psychology, University College London, London, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4848-7167
  9. Thomas Wheatcroft

    Experimental Psychology, University College London, London, United Kingdom
    Competing interests
    No competing interests declared.
  10. Stefano Zucca

    Experimental Psychology, University College London, London, United Kingdom
    Competing interests
    No competing interests declared.
  11. Samuel G Solomon

    Experimental Psychology, University College London, London, United Kingdom
    For correspondence
    s.solomon@ucl.ac.uk
    Competing interests
    No competing interests declared.
  12. Aman B Saleem

    Experimental Psychology, University College London, London, United Kingdom
    For correspondence
    aman.saleem@ucl.ac.uk
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7100-1954

Funding

Wellcome Trust (200501)

  • Aman B Saleem

Human Frontiers in Science Program (RGY0076/2018)

  • Aman B Saleem

Stavros Niarchos Foundation / Research to Prevent Blindness

  • Samuel G Solomon

Medical Research Council (R023808)

  • Samuel G Solomon
  • Aman B Saleem

Biotechnology and Biological Sciences Research Council (R004765)

  • Samuel G Solomon
  • Aman B Saleem

Wellcome Trust: OPen Research (200501/Z/16/A)

  • Aman B Saleem

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All experiments were performed in accordance with the Animals (Scientific Procedures) Act 1986 (United Kingdom) and Home Office (United Kingdom) approved project and personal licenses. The experiments were approved by the University College London Animal Welfare Ethical Review Board under Project License 70/8637.

Human subjects: All procedures were approved by the Experimental Psychology Ethics Committee at University College London (Ethics Application EP/2019/002). We obtained informed consent, and consent to publish from all participants.

Reviewing Editor

  1. Chris I Baker, National Institute of Mental Health, National Institutes of Health, United States

Publication history

  1. Received: December 7, 2020
  2. Accepted: April 20, 2021
  3. Accepted Manuscript published: April 21, 2021 (version 1)
  4. Version of Record published: May 7, 2021 (version 2)
  5. Version of Record updated: May 19, 2021 (version 3)

Copyright

© 2021, Lopes et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Gonçalo Lopes
  2. Karolina Farrell
  3. Edward A B Horrocks
  4. Chi Yu Lee
  5. Mai M Morimoto
  6. Tomaso Muzzu
  7. Amalia Papanikolaou
  8. Fabio R Rodrigues
  9. Thomas Wheatcroft
  10. Stefano Zucca
  11. Samuel G Solomon
  12. Aman B Saleem
(2021)
Creating and controlling visual environments using BonVision
eLife 10:e65541.
https://doi.org/10.7554/eLife.65541

Further reading

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    Theta and gamma oscillations in the medial temporal lobe are suggested to play a critical role for human memory formation via establishing synchrony in neural assemblies. Arguably, such synchrony facilitates efficient information transfer between neurons and enhances synaptic plasticity, both of which benefit episodic memory formation. However, to date little evidence exists from humans that would provide direct evidence for such a specific role of theta and gamma oscillations for episodic memory formation. Here, we investigate how oscillations shape the temporal structure of neural firing during memory formation in the medial temporal lobe. We measured neural firing and local field potentials in human epilepsy patients via micro-wire electrode recordings to analyze whether brain oscillations are related to co-incidences of firing between neurons during successful and unsuccessful encoding of episodic memories. The results show that phase-coupling of neurons to faster theta and gamma oscillations correlates with co-firing at short latencies (~20–30 ms) and occurs during successful memory formation. Phase-coupling at slower oscillations in these same frequency bands, in contrast, correlates with longer co-firing latencies and occurs during memory failure. Thus, our findings suggest that neural oscillations play a role for the synchronization of neural firing in the medial temporal lobe during the encoding of episodic memories.

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