Literature DB >> 35043782

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

Rui M Costa1,2, Mark E Walton3,4, Thomas Akam3,1, Andy Lustig5, James M Rowland6, Sampath Kt Kapanaiah7, Joan Esteve-Agraz8, Mariangela Panniello6,9, Cristina Márquez8, Michael M Kohl6,9, Dennis Kätzel7.   

Abstract

Laboratory behavioural tasks are an essential research tool. As questions asked of behaviour and brain activity become more sophisticated, the ability to specify and run richly structured tasks becomes more important. An increasing focus on reproducibility also necessitates accurate communication of task logic to other researchers. To these ends, we developed pyControl, a system of open-source hardware and software for controlling behavioural experiments comprising a simple yet flexible Python-based syntax for specifying tasks as extended state machines, hardware modules for building behavioural setups, and a graphical user interface designed for efficiently running high-throughput experiments on many setups in parallel, all with extensive online documentation. These tools make it quicker, easier, and cheaper to implement rich behavioural tasks at scale. As important, pyControl facilitates communication and reproducibility of behavioural experiments through a highly readable task definition syntax and self-documenting features. Here, we outline the system's design and rationale, present validation experiments characterising system performance, and demonstrate example applications in freely moving and head-fixed mouse behaviour.
© 2022, Akam et al.

Entities:  

Keywords:  Behaviour; Hardware; Software; mouse; neuroscience; open source

Mesh:

Year:  2022        PMID: 35043782      PMCID: PMC8769647          DOI: 10.7554/eLife.67846

Source DB:  PubMed          Journal:  Elife        ISSN: 2050-084X            Impact factor:   8.140


  28 in total

1.  Two open source designs for a low-cost operant chamber using Raspberry Pi™.

Authors:  Katelyn Gurley
Journal:  J Exp Anal Behav       Date:  2019-04-30       Impact factor: 2.468

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

Authors:  Jai Bhagat; Miles J Wells; Kenneth D Harris; Matteo Carandini; Christopher P Burgess
Journal:  eNeuro       Date:  2020-07-09

3.  A low-cost touchscreen operant chamber using a Raspberry Pi™.

Authors:  James D O'Leary; Olivia F O'Leary; John F Cryan; Yvonne M Nolan
Journal:  Behav Res Methods       Date:  2018-12

4.  Open-source raspberry Pi-based operant box for translational behavioral testing in rodents.

Authors:  N Buscher; A Ojeda; M Francoeur; S Hulyalkar; C Claros; T Tang; A Terry; A Gupta; L Fakhraei; D S Ramanathan
Journal:  J Neurosci Methods       Date:  2020-05-30       Impact factor: 2.390

5.  Effects of atomoxetine and methylphenidate on attention and impulsivity in the 5-choice serial reaction time test.

Authors:  Rachel Navarra; Radka Graf; Youping Huang; Sheree Logue; Thomas Comery; Zoe Hughes; Mark Day
Journal:  Prog Neuropsychopharmacol Biol Psychiatry       Date:  2007-06-27       Impact factor: 5.067

6.  Effects of lesions to ascending noradrenergic neurones on performance of a 5-choice serial reaction task in rats; implications for theories of dorsal noradrenergic bundle function based on selective attention and arousal.

Authors:  M Carli; T W Robbins; J L Evenden; B J Everitt
Journal:  Behav Brain Res       Date:  1983-09       Impact factor: 3.332

7.  The haves and the have nots.

Authors:  Eve Marder
Journal:  Elife       Date:  2013-11-19       Impact factor: 8.140

8.  Layer-specific integration of locomotion and sensory information in mouse barrel cortex.

Authors:  Aslı Ayaz; Andreas Stäuble; Morio Hamada; Marie-Angela Wulf; Aman B Saleem; Fritjof Helmchen
Journal:  Nat Commun       Date:  2019-06-13       Impact factor: 14.919

9.  Real-time experimental control using network-based parallel processing.

Authors:  Byounghoon Kim; Shobha Channabasappa Kenchappa; Adhira Sunkara; Ting-Yu Chang; Lowell Thompson; Raymond Doudlah; Ari Rosenberg
Journal:  Elife       Date:  2019-02-07       Impact factor: 8.140

10.  A low-cost open-source 5-choice operant box system optimized for electrophysiology and optophysiology in mice.

Authors:  Thomas Akam; Dennis Kätzel; Sampath K T Kapanaiah; Bastiaan van der Veen; Daniel Strahnen
Journal:  Sci Rep       Date:  2021-11-15       Impact factor: 4.379

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  2 in total

1.  Distinct contributions of GluA1-containing AMPA receptors of different hippocampal subfields to salience processing, memory and impulse control.

Authors:  Kasyoka Kilonzo; Daniel Strahnen; Vivien Prex; John Gems; Bastiaan van der Veen; Sampath K T Kapanaiah; Bhargavi K B Murthy; Stefanie Schulz; Rolf Sprengel; David Bannerman; Dennis Kätzel
Journal:  Transl Psychiatry       Date:  2022-03-14       Impact factor: 7.989

2.  Complementary task representations in hippocampus and prefrontal cortex for generalizing the structure of problems.

Authors:  Timothy E J Behrens; Thomas Akam; Veronika Samborska; James L Butler; Mark E Walton
Journal:  Nat Neurosci       Date:  2022-09-28       Impact factor: 28.771

  2 in total

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