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

Nicholas C. Guilbeault, Jordan Guerguiev, Michael Martin, Isabelle Tate, Tod R. Thiele
doi: https://doi.org/10.1101/2021.03.02.433632
Nicholas C. Guilbeault
1Department of Biological Sciences, University of Toronto Scarborough
2Department of Cell and Systems Biology, University of Toronto
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Jordan Guerguiev
1Department of Biological Sciences, University of Toronto Scarborough
2Department of Cell and Systems Biology, University of Toronto
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Michael Martin
1Department of Biological Sciences, University of Toronto Scarborough
2Department of Cell and Systems Biology, University of Toronto
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Isabelle Tate
1Department of Biological Sciences, University of Toronto Scarborough
2Department of Cell and Systems Biology, University of Toronto
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Tod R. Thiele
1Department of Biological Sciences, University of Toronto Scarborough
2Department of Cell and Systems Biology, University of Toronto
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  • For correspondence: tod.thiele@utoronto.ca
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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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/ncguilbeault/BonZeb

  • https://git.io/JJABI

  • https://git.io/JtMIo

  • https://git.io/JtMIi

  • https://git.io/JtyBW

  • https://git.io/JtyBB

  • https://git.io/JtyBz

  • https://git.io/JtyB2

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 02, 2021.
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BonZeb: Open-source, modular software tools for high-resolution zebrafish tracking and analysis
Nicholas C. Guilbeault, Jordan Guerguiev, Michael Martin, Isabelle Tate, Tod R. Thiele
bioRxiv 2021.03.02.433632; doi: https://doi.org/10.1101/2021.03.02.433632
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BonZeb: Open-source, modular software tools for high-resolution zebrafish tracking and analysis
Nicholas C. Guilbeault, Jordan Guerguiev, Michael Martin, Isabelle Tate, Tod R. Thiele
bioRxiv 2021.03.02.433632; doi: https://doi.org/10.1101/2021.03.02.433632

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