Introduction

Welcome to BonZeb - a Bonsai library for behavioural tracking and stimulation of zebrafish and other model organisms.

BonZeb is a Bonsai library for high-resolution behavioural tracking and stimulation. BonZeb provides essential tools for zebrafish behavioural tracking and analysis. Here, you will find information and examples for how to use BonZeb to implement behavioural analysis, multi-animal tracking, closed-loop and virtual open-loop visual stimulation, and more.

Download

This package was originally built in Bonsai version 2.4.0 but should work for newer versions of Bonsai as well. You can download the latest version of Bonsai or download earlier versions here. BonZeb can be easily downloaded using Bonsai’s built-in package manager. BonZeb can also be added to Bonsai manually by downloading the GitHub Repository and adding it to the package manager. To add the package manually to the package manager, navigate to settings and add the .nuget folder of the repository to the list of available package sources.

Dependencies

When installing BonZeb, all of the essential dependencies will be installed automatically. However, some of the example workflows draw from other non-dependant Bonsai libraries. These libraries include:

Bonsai - Arduino Library
Bonsai - Core Library
Bonsai - Design Library
Bonsai - Dsp Library
Bonsai - Dsp Design Library
Bonsai - Editor
Bonsai - Player
Bonsai - Scripting Library
Bonsai - Shaders Library
Bonsai - Shaders Design Library
Bonsai - System Library
Bonsai - System Design Library
Bonsai - Video Library
Bonsai - Video Design Library
Bonsai - Vision Library
Bonsai - Vision Design Library
Bonsai - Windows Input Library

Getting Started with Bonsai

Bonsai is a powerful programming language with a visual programming interface that uses graphs, also called workflows, to represent data processing pipelines in the interactive development environement (IDE). The nodes in a Bonsai workflow, also called modules, can represent a variety of different Bonsai objects, such as data sources, transformations, combinators, or sinks. Modules in a workflow are linked by edges to form pipelines, also called data streams, where the output of one node is sent as input to another node. The basic premise for building Bonsai workflows is adding nodes into the workflow and connecting nodes together to form pipelines or data streams. Data streams can be split and merged together in various ways such that the final workflow can have multiple data streams operating synchronously or asynchronously, simultaneously.

If you are using Bonsai for the first time, check out Basics to learn more. If you are already familiar with Bonsai and how it works, feel free to skip this section.

Video Acquisition

BonZeb is completely modular and works with any camera module alreay supported in Bonsai (Basler, FLIR, DirectShow, etc.). Additionally, BonZeb interfaces with Allied Vision, Teledyne Dalsa, and Euresys CameraLink Frame Grabber hardware devices for high-speed video acquisition. The following video acqusition packages are available for download:

Users must install the manufacturers software development kit (SDK) and ensure the camera is connected to the computer and working properly before using the camera in Bonsai. Both the Allied Vision and Teledyne Dalsa modules require bonsai to be run in no boot mode. To do this, Bonsai must be started from the command line with the following argument:

Bonsai.exe --noboot

Tools, Workflows, and Applications

BonZeb is fully modular and easily slots into custom Bonsai workflows. Here are a few examples of the types of applications using BonZeb.

Acknowledgements

Thank you to all of the people who tested BonZeb and provided useful feedback on the manuscript. Thank you to the developers for creating the elegant and powerful programming language Bonsai and to the larger community for welcoming the exchange of ideas.