Cargando…

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

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Akam, Thomas, Lustig, Andy, Rowland, James M, Kapanaiah, Sampath KT, Esteve-Agraz, Joan, Panniello, Mariangela, Márquez, Cristina, Kohl, Michael M, Kätzel, Dennis, Costa, Rui M, Walton, Mark E
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8769647/
https://www.ncbi.nlm.nih.gov/pubmed/35043782
http://dx.doi.org/10.7554/eLife.67846
_version_ 1784635196102934528
author Akam, Thomas
Lustig, Andy
Rowland, James M
Kapanaiah, Sampath KT
Esteve-Agraz, Joan
Panniello, Mariangela
Márquez, Cristina
Kohl, Michael M
Kätzel, Dennis
Costa, Rui M
Walton, Mark E
author_facet Akam, Thomas
Lustig, Andy
Rowland, James M
Kapanaiah, Sampath KT
Esteve-Agraz, Joan
Panniello, Mariangela
Márquez, Cristina
Kohl, Michael M
Kätzel, Dennis
Costa, Rui M
Walton, Mark E
author_sort Akam, Thomas
collection PubMed
description 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.
format Online
Article
Text
id pubmed-8769647
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher eLife Sciences Publications, Ltd
record_format MEDLINE/PubMed
spelling pubmed-87696472022-01-21 Open-source, Python-based, hardware and software for controlling behavioural neuroscience experiments Akam, Thomas Lustig, Andy Rowland, James M Kapanaiah, Sampath KT Esteve-Agraz, Joan Panniello, Mariangela Márquez, Cristina Kohl, Michael M Kätzel, Dennis Costa, Rui M Walton, Mark E eLife Neuroscience 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. eLife Sciences Publications, Ltd 2022-01-19 /pmc/articles/PMC8769647/ /pubmed/35043782 http://dx.doi.org/10.7554/eLife.67846 Text en © 2022, Akam et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Neuroscience
Akam, Thomas
Lustig, Andy
Rowland, James M
Kapanaiah, Sampath KT
Esteve-Agraz, Joan
Panniello, Mariangela
Márquez, Cristina
Kohl, Michael M
Kätzel, Dennis
Costa, Rui M
Walton, Mark E
Open-source, Python-based, hardware and software for controlling behavioural neuroscience experiments
title Open-source, Python-based, hardware and software for controlling behavioural neuroscience experiments
title_full Open-source, Python-based, hardware and software for controlling behavioural neuroscience experiments
title_fullStr Open-source, Python-based, hardware and software for controlling behavioural neuroscience experiments
title_full_unstemmed Open-source, Python-based, hardware and software for controlling behavioural neuroscience experiments
title_short Open-source, Python-based, hardware and software for controlling behavioural neuroscience experiments
title_sort open-source, python-based, hardware and software for controlling behavioural neuroscience experiments
topic Neuroscience
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8769647/
https://www.ncbi.nlm.nih.gov/pubmed/35043782
http://dx.doi.org/10.7554/eLife.67846
work_keys_str_mv AT akamthomas opensourcepythonbasedhardwareandsoftwareforcontrollingbehaviouralneuroscienceexperiments
AT lustigandy opensourcepythonbasedhardwareandsoftwareforcontrollingbehaviouralneuroscienceexperiments
AT rowlandjamesm opensourcepythonbasedhardwareandsoftwareforcontrollingbehaviouralneuroscienceexperiments
AT kapanaiahsampathkt opensourcepythonbasedhardwareandsoftwareforcontrollingbehaviouralneuroscienceexperiments
AT esteveagrazjoan opensourcepythonbasedhardwareandsoftwareforcontrollingbehaviouralneuroscienceexperiments
AT panniellomariangela opensourcepythonbasedhardwareandsoftwareforcontrollingbehaviouralneuroscienceexperiments
AT marquezcristina opensourcepythonbasedhardwareandsoftwareforcontrollingbehaviouralneuroscienceexperiments
AT kohlmichaelm opensourcepythonbasedhardwareandsoftwareforcontrollingbehaviouralneuroscienceexperiments
AT katzeldennis opensourcepythonbasedhardwareandsoftwareforcontrollingbehaviouralneuroscienceexperiments
AT costaruim opensourcepythonbasedhardwareandsoftwareforcontrollingbehaviouralneuroscienceexperiments
AT waltonmarke opensourcepythonbasedhardwareandsoftwareforcontrollingbehaviouralneuroscienceexperiments