BonZeb: open-source, modular software tools for high-resolution zebrafish tracking and analysis

Abstract We present BonZeb—a suite of modular Bonsai packages which allow high-resolution zebrafish tracking with dynamic visual feedback. Bonsai is an increasingly popular software platform that is accelerating the standardization of experimental protocols within the neurosciences due to its speed,...

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Autores principales:	Nicholas C. Guilbeault, Jordan Guerguiev, Michael Martin, Isabelle Tate, Tod R. Thiele
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4db63489e21547e4ac081d3df7264747
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spelling	oai:doaj.org-article:4db63489e21547e4ac081d3df72647472021-12-02T14:30:46ZBonZeb: open-source, modular software tools for high-resolution zebrafish tracking and analysis10.1038/s41598-021-85896-x2045-2322https://doaj.org/article/4db63489e21547e4ac081d3df72647472021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-85896-xhttps://doaj.org/toc/2045-2322Abstract We present BonZeb—a suite of modular Bonsai packages which allow high-resolution zebrafish tracking with dynamic visual feedback. Bonsai is an increasingly popular software platform that is accelerating the standardization of experimental protocols within the neurosciences due to its speed, flexibility, and minimal programming overhead. BonZeb can be implemented into novel and existing Bonsai workflows for online behavioral tracking and offline tracking with batch processing. We demonstrate that BonZeb can run a variety of experimental configurations used for gaining insights into the neural mechanisms of zebrafish behavior. BonZeb supports head-fixed closed-loop and free-swimming virtual open-loop assays as well as multi-animal tracking, optogenetic stimulation, and calcium imaging during behavior. The combined performance, ease of use and versatility of BonZeb opens new experimental avenues for researchers seeking high-resolution behavioral tracking of larval zebrafish.Nicholas C. GuilbeaultJordan GuerguievMichael MartinIsabelle TateTod R. ThieleNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-21 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nicholas C. Guilbeault Jordan Guerguiev Michael Martin Isabelle Tate Tod R. Thiele BonZeb: open-source, modular software tools for high-resolution zebrafish tracking and analysis
description	Abstract We present BonZeb—a suite of modular Bonsai packages which allow high-resolution zebrafish tracking with dynamic visual feedback. Bonsai is an increasingly popular software platform that is accelerating the standardization of experimental protocols within the neurosciences due to its speed, flexibility, and minimal programming overhead. BonZeb can be implemented into novel and existing Bonsai workflows for online behavioral tracking and offline tracking with batch processing. We demonstrate that BonZeb can run a variety of experimental configurations used for gaining insights into the neural mechanisms of zebrafish behavior. BonZeb supports head-fixed closed-loop and free-swimming virtual open-loop assays as well as multi-animal tracking, optogenetic stimulation, and calcium imaging during behavior. The combined performance, ease of use and versatility of BonZeb opens new experimental avenues for researchers seeking high-resolution behavioral tracking of larval zebrafish.
format	article
author	Nicholas C. Guilbeault Jordan Guerguiev Michael Martin Isabelle Tate Tod R. Thiele
author_facet	Nicholas C. Guilbeault Jordan Guerguiev Michael Martin Isabelle Tate Tod R. Thiele
author_sort	Nicholas C. Guilbeault
title	BonZeb: open-source, modular software tools for high-resolution zebrafish tracking and analysis
title_short	BonZeb: open-source, modular software tools for high-resolution zebrafish tracking and analysis
title_full	BonZeb: open-source, modular software tools for high-resolution zebrafish tracking and analysis
title_fullStr	BonZeb: open-source, modular software tools for high-resolution zebrafish tracking and analysis
title_full_unstemmed	BonZeb: open-source, modular software tools for high-resolution zebrafish tracking and analysis
title_sort	bonzeb: open-source, modular software tools for high-resolution zebrafish tracking and analysis
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/4db63489e21547e4ac081d3df7264747
work_keys_str_mv	AT nicholascguilbeault bonzebopensourcemodularsoftwaretoolsforhighresolutionzebrafishtrackingandanalysis AT jordanguerguiev bonzebopensourcemodularsoftwaretoolsforhighresolutionzebrafishtrackingandanalysis AT michaelmartin bonzebopensourcemodularsoftwaretoolsforhighresolutionzebrafishtrackingandanalysis AT isabelletate bonzebopensourcemodularsoftwaretoolsforhighresolutionzebrafishtrackingandanalysis AT todrthiele bonzebopensourcemodularsoftwaretoolsforhighresolutionzebrafishtrackingandanalysis
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BonZeb: open-source, modular software tools for high-resolution zebrafish tracking and analysis

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