Literature DB >> 32493756

Rigbox: An Open-Source Toolbox for Probing Neurons and Behavior.

Jai Bhagat1, Miles J Wells2,3, Kenneth D Harris2, Matteo Carandini3, Christopher P Burgess3.   

Abstract

Setting up an experiment in behavioral neuroscience is a complex process that is often managed with ad hoc solutions. To streamline this process, we developed Rigbox, a high-performance, open-source software toolbox that facilitates a modular approach to designing experiments (https://github.com/cortex-lab/Rigbox). Rigbox simplifies hardware input-output, time aligns datastreams from multiple sources, communicates with remote databases, and implements visual and auditory stimuli presentation. Its main submodule, Signals, allows intuitive programming of behavioral tasks. Here we illustrate its function with the following two interactive examples: a human psychophysics experiment, and the game of Pong. We give an overview of running experiments in Rigbox, provide benchmarks, and conclude with a discussion on the extensibility of the software and comparisons with similar toolboxes. Rigbox runs in MATLAB, with Java components to handle network communication, and a C library to boost performance.
Copyright © 2020 Bhagat et al.

Entities:  

Keywords:  behavioral; control; experimental; software; toolbox

Mesh:

Year:  2020        PMID: 32493756      PMCID: PMC7363478          DOI: 10.1523/ENEURO.0406-19.2020

Source DB:  PubMed          Journal:  eNeuro        ISSN: 2373-2822


  10 in total

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Authors:  James J Jun; Nicholas A Steinmetz; Joshua H Siegle; Daniel J Denman; Marius Bauza; Brian Barbarits; Albert K Lee; Costas A Anastassiou; Alexandru Andrei; Çağatay Aydın; Mladen Barbic; Timothy J Blanche; Vincent Bonin; João Couto; Barundeb Dutta; Sergey L Gratiy; Diego A Gutnisky; Michael Häusser; Bill Karsh; Peter Ledochowitsch; Carolina Mora Lopez; Catalin Mitelut; Silke Musa; Michael Okun; Marius Pachitariu; Jan Putzeys; P Dylan Rich; Cyrille Rossant; Wei-Lung Sun; Karel Svoboda; Matteo Carandini; Kenneth D Harris; Christof Koch; John O'Keefe; Timothy D Harris
Journal:  Nature       Date:  2017-11-08       Impact factor: 49.962

Review 3.  Probing perceptual decisions in rodents.

Authors:  Matteo Carandini; Anne K Churchland
Journal:  Nat Neurosci       Date:  2013-06-25       Impact factor: 24.884

4.  Engagement of neural circuits underlying 2D spatial navigation in a rodent virtual reality system.

Authors:  Dmitriy Aronov; David W Tank
Journal:  Neuron       Date:  2014-10-22       Impact factor: 17.173

Review 5.  An International Laboratory for Systems and Computational Neuroscience.

Authors: 
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6.  High-Yield Methods for Accurate Two-Alternative Visual Psychophysics in Head-Fixed Mice.

Authors:  Christopher P Burgess; Armin Lak; Nicholas A Steinmetz; Peter Zatka-Haas; Charu Bai Reddy; Elina A K Jacobs; Jennifer F Linden; Joseph J Paton; Adam Ranson; Sylvia Schröder; Sofia Soares; Miles J Wells; Lauren E Wool; Kenneth D Harris; Matteo Carandini
Journal:  Cell Rep       Date:  2017-09-05       Impact factor: 9.423

7.  The impact of bilateral ongoing activity on evoked responses in mouse cortex.

Authors:  Daisuke Shimaoka; Nicholas A Steinmetz; Kenneth D Harris; Matteo Carandini
Journal:  Elife       Date:  2019-04-30       Impact factor: 8.140

8.  Dopaminergic and Prefrontal Basis of Learning from Sensory Confidence and Reward Value.

Authors:  Armin Lak; Michael Okun; Morgane M Moss; Harsha Gurnani; Karolina Farrell; Miles J Wells; Charu Bai Reddy; Adam Kepecs; Kenneth D Harris; Matteo Carandini
Journal:  Neuron       Date:  2019-12-16       Impact factor: 17.173

9.  Distributed coding of choice, action and engagement across the mouse brain.

Authors:  Nicholas A Steinmetz; Peter Zatka-Haas; Matteo Carandini; Kenneth D Harris
Journal:  Nature       Date:  2019-11-27       Impact factor: 49.962

10.  Cortical State Fluctuations during Sensory Decision Making.

Authors:  Elina A K Jacobs; Nicholas A Steinmetz; Andrew J Peters; Matteo Carandini; Kenneth D Harris
Journal:  Curr Biol       Date:  2020-10-22       Impact factor: 10.834

  10 in total
  7 in total

1.  Creating and controlling visual environments using BonVision.

Authors:  Samuel G Solomon; Aman B Saleem; Gonçalo Lopes; Karolina Farrell; Edward Ab Horrocks; Chi-Yu Lee; Mai M Morimoto; Tomaso Muzzu; Amalia Papanikolaou; Fabio R Rodrigues; Thomas Wheatcroft; Stefano Zucca
Journal:  Elife       Date:  2021-04-21       Impact factor: 8.140

2.  Open-source, Python-based, hardware and software for controlling behavioural neuroscience experiments.

Authors:  Rui M Costa; Mark E Walton; Thomas Akam; Andy Lustig; James M Rowland; Sampath Kt Kapanaiah; Joan Esteve-Agraz; Mariangela Panniello; Cristina Márquez; Michael M Kohl; Dennis Kätzel
Journal:  Elife       Date:  2022-01-19       Impact factor: 8.140

3.  Neural correlates of blood flow measured by ultrasound.

Authors:  Anwar O Nunez-Elizalde; Michael Krumin; Charu Bai Reddy; Gabriel Montaldo; Alan Urban; Kenneth D Harris; Matteo Carandini
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4.  A low-cost open-source 5-choice operant box system optimized for electrophysiology and optophysiology in mice.

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5.  Sensory coding and the causal impact of mouse cortex in a visual decision.

Authors:  Peter Zatka-Haas; Nicholas A Steinmetz; Matteo Carandini; Kenneth D Harris
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6.  Dopamine Axons in Dorsal Striatum Encode Contralateral Visual Stimuli and Choices.

Authors:  Morgane M Moss; Peter Zatka-Haas; Kenneth D Harris; Matteo Carandini; Armin Lak
Journal:  J Neurosci       Date:  2021-07-12       Impact factor: 6.167

7.  Striatal activity topographically reflects cortical activity.

Authors:  Andrew J Peters; Julie M J Fabre; Nicholas A Steinmetz; Kenneth D Harris; Matteo Carandini
Journal:  Nature       Date:  2021-01-20       Impact factor: 49.962

  7 in total

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