This project is licensed under the GNU General Public License v3.0
The hardware is licensed under the CERN OHL v1.2
This project aims to investigate the larval zebrafish behavioural responses to spatio-chromatic stimulation in a free-swimming environment. The "Thunderdome"© is a stimulation system designed to experiment on the tetra-chromatic larval zebrafish. It is therefore designed around 4 set of LEDs (each LED matching the zebrafish' opsins peak absorption Zimmermann et al. 2018 & Zimmermann et al. 2020, organised in 8 cardinal directions and 4 azimuths. Using machine-learning algorithms, fish motor responses (body direction, eyes orientation, tail kinetics, etc.) are identified and compared to well-known behavioural catalogs ref . The purpose of this project is to identify behavioural responses to specific spatio-chromatic stimulation which were/are studied in early visual system under two photon microscopy ref,ref,ref
- An open and versatile LED controler
- A semi-automated behavioural tracking
- A detailed assembly and instruction manual
- Required software
- Repository Structure
bonsai
For tracking the larval zebrafish movements, we are considering two different approaches:
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DeepLabCut, a toolbox for markerless pose estimation based on transfer learning with deep neural networks that achieves excellent results with minimal training data Mathis et al. 2018, Nath & Mathis 2019.
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BonZeb, a Bonsai library for high-resolution zebrafish behavioural tracking and analysis Guilbeault 2019
├───3D Designs Contains printed parts for the stimulator
| ├───FreeCad renderings - Printing files
| ├───STL files - Printing files
| └───SCAD files - SCAD files to be modified if need be
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├───Arduino Code Stimulator Code
| ├───Stimulator Code - Adaptable C+ code for running the stimulator
| └───LED driver library - Library to run the TLC 5947
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├───Bill of Materials List of necessary components and retailer suggestions
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├───Bonsai code Bonsai pipeline for running the stimulation and export data
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├───Datasheets - Contains all technical sheet for:
| ├───Stimulator - ...micro-controller and LED driver
| └───Spectrometer - ...device used for calibration
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├───Images Image repository
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├───Instruction Manual Detailed manual to assemble and calibrate the stimulator
| └───Stimulator Calibration - Contains calibration recordings and the adaptable jupyter notebook script to calibrate the stimulator
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├───PCB KiCad and Gerber files to modify and generate PCB
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└───References Publication used to design and conceive this model