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Download ZebraZoom.

ZebraZoom is open-source and can be downloaded and used free of charge: feel free to use it for your research and please acknowledge us in your publications.

In all your publications that make use of ZebraZoom:

First and foremost, please acknowledge Claire Wyart's lab that has been supporting the development of ZebraZoom for many years.

Please also cite the original ZebraZoom paper.

Please also mention this website (zebrazoom.org) and/or our github repository (github.com/oliviermirat/ZebraZoom).

Alternatively, you can also download ZebraZoom through the Anaconda Installation on Windows, Mac and Linux.

Download test videos here!

Our software can be used for videos with a fixed background to track the heads and tails of freely swimming and of head-embedded zebrafish as well as the center of mass of any kind of animal.


Founding Team

Olivier Mirat

Olivier is a software engineer and data scientist who has been working at the interface of biology and computer science for over a decade. In Virginia Tech he worked in a bioinformatics lab and participated in the creation of bio-security software for DNA sequence screening that he later presented along with his teammates at the iGEM competition and at the FBI headquarters. He has also worked in an early stage digital health startup in San Francisco creating a web-based chatbot relying on an AI medical diagnosis engine and has worked on other independent digital health projects. Olivier started working on ZebraZoom during his PhD in Claire Wyart’s lab in Paris and now wants to make other labs and corporations around the world benefit from his many years of experience analyzing the behavior of zebrafish larvae.

Claire Wyart

During her PhD, Claire developed novel methods for controlling the architecture of neuronal networks in vitro and demonstrated mechanisms underlying the emergence of spontaneous activity. She joined UC Berkeley for her postdoctoral fellowship and developed optogenetic methods in vivo by taking advantage of the transparency of the zebrafish larva. In this small vertebrate model, Claire used optogenetics to study sensory-motor integration, analyzing the processing of visual, mechanosensory and chemosensory pathways modulating locomotion. Since 2011, Claire started her team at the Brain and Spinal cord Institute in Paris. She is interested in deciphering the neuronal circuits that integrate information from the brain, from the periphery and from internal cues in order to modulate locomotion and posture as a function of inner physiological states.

Research Labs that have supported the development of ZebraZoom

Wyart Lab, Brain Institute, Paris, France

(Primary lab behind ZebraZoom, since 2010 and until now)

The Wyart lab was responsible for initially starting the ZebraZoom project and has provided the vast majority of the funding necessary for the development of this software. Wyart lab team members were also vastly responsible for testing and giving feedback on ZebraZoom. The Wyart lab opened up all major axis of ZebraZoom's development and to this day, it remains the main lab responsible for pushing the development of the software on all fronts: tracking, kinematic data analysis pipeline, GUI (Graphical User Interface), and further innovations.

Nicolson Lab, Stanford University, United States

The Nicolson lab provided funding to push some of the development of head-embedded fish tail tracking. The Nicolson lab also got involved at a time when the development of ZebraZoom's GUI was just getting started and was only working with limited features on Windows and Linux only: their involvement was critical and very beneficial in creating a better version of the GUI that would also work on Mac.

Song Lab, Tongji University, Shanghai, China

The Song lab provided funding to create scripts to analyze sleeping and moving activity in fish. They are also mainly responsible for supporting the development of the newest "Fast and easy screen for any kind of animal" option in the configuration file creation system. This option allows a very fast and efficient tracking of animals' center of mass and can be used for genetic and drug screens as a free open-source replacement to commercially available systems.

Further Acknowledgments

We would like to thank Ante Sikic for developing the newest graphical user interface of ZebraZoom. We would also like to thank Feng Quan, Laura Desban, Martin Carbó-Tano, Mathilde Lapoix, Mingyue Wu, Adna Dumitrescu, Jenna Sternberg, Maxime Kermarquer, Maha Dhanasekar, Gautam Sridhar, Xinyu Jia, Julian Roussel, Teresa Nicolson, Yan Gao, Biswadeep Khan, Jane Yam, Na Guan and Jianren Song for letting us use the videos they've captured and for their help with the development of ZebraZoom. We would also like to thank Thomas Preat's lab and Nicolas Renier's lab for letting us use the videos they've captured.

Papers published that have used ZebraZoom:

Not from Claire Wyart's lab:

Sensory deficit screen identifies nsf mutation that differentially affects SNARE recycling and quality control. Yan Gao, Yousuf A Khan, Weike Mo, K Ian White, Matthew Perkins, Richard A Pfuetzner, Josef G Trapani, Axel T Brunger, Teresa Nicolson - Cell Reports, 2023

A novel PLS1 c. 981+ 1G> A variant causes autosomal‐dominant hereditary hearing loss in a family Liangpu Xu, Xinrui Wang, Jia Li, Lingji Chen, Haiwei Wang, Shiyi Xu, Yanhong Zhang, Wei Li, Pengcheng Yao, Meihua Tan, Si Zhou, Meihuan Chen, Yali Pan, Xuemei Chen, Xiaolan Chen, Yunliang Liu, Na Lin, Hailong Huang, Hua Cao - Clinical Genetics, Wiley Online Library, 2023

Organization of the gravity-sensing system in zebrafish.Zhikai Liu, David G C Hildebrand, Joshua L Morgan, Yizhen Jia, Nicholas Slimmon, Martha W Bagnall - Nature Communications, 2022

De novo establishment of circuit modules restores locomotion after spinal cord injury in adult zebrafish. Chun-Xiao Huang, Zhen Wang, Jianwei Cheng , Zhiqiang Zhu, Na N Guan, Jianren Song - Cell Reports, 2022

Temporal Vestibular Deficits in synaptojanin 1 (synj1) Mutants. Yan Gao, Teresa Nicolson - Frontiers in Molecular Neuroscience, 2021

An injury-induced serotonergic neuron subpopulation contributes to axon regrowth and function restoration after spinal cord injury in zebrafish. Chun-Xiao Huang, Yacong Zhao, Jie Mao, Zhen Wang, Lulu Xu, Jianwei Cheng, Na N Guan, Jianren Song - Nature Communications, 2021

A neuronal circuit that generates the temporal motor sequence for the defensive response in zebrafish larvae. Lulu Xu, Na N. Guan, Chun-Xiao Huang, Yunfeng Hua, Jianren Song - Current Biology, 2021

From Claire Wyart's lab:

The mesencephalic locomotor region recruits V2a reticulospinal neurons to drive forward locomotion in larval zebrafish. Martin Carbo-Tano, Mathilde Lapoix, Xinyu Jia, Olivier Thouvenin, Marco Pascucci, François Auclair, Feng B Quan, Shahad Albadri, Vernie Aguda, Younes Farouj, Elizabeth M C Hillman, Ruben Portugues, Filippo Del Bene, Tod R Thiele, Réjean Dubuc, Claire Wyart - Nature neuroscience, 2023

CSF-contacting neurons respond to Streptococcus pneumoniae and promote host survival during central nervous system infection. Andrew E Prendergast, Kin Ki Jim, Hugo Marnas, Laura Desban, Feng B Quan, Lydia Djenoune, Valerio Laghi, Agnès Hocquemiller, Elias T Lunsford, Julian Roussel, Ludovic Keiser, Francois-Xavier Lejeune, Mahalakshmi Dhanasekar, Pierre-Luc Bardet, Jean-Pierre Levraud, Diederik van de Beek, Christina M J E Vandenbroucke-Grauls, Claire Wyart - Current Biology, 2023

Lateral line hair cells integrate mechanical and chemical cues to orient navigation. Laura Desban, Julian Roussel, Olivier Mirat, François-Xavier Lejeune, Ludovic Keiser, Nicolas Michalski, Claire Wyart - bioRxiv, 2022

A lexical approach for identifying behavioural action sequences. Gautam Reddy, Laura Desban, Hidenori Tanaka, Julian Roussel, Olivier Mirat, Claire Wyart - PLoS Computational Biology, 2022

Spinal sensory neurons project onto the hindbrain to stabilize posture and enhance locomotor speed. Ming-Yue Wu, Martin Carbo-Tano, Olivier Mirat, Francois-Xavier Lejeune, Julian Roussel, Feng B Quan, Kevin Fidelin, Claire Wyart - Current Biology, 2021 - cell.com

Somatostatin 1.1 contributes to the innate exploration of zebrafish larva.Feng B Quan, Laura Desban, Olivier Mirat, Maxime Kermarquer, Julian Roussel, Fanny Koëth, Hugo Marnas, Lydia Djenoune, François-Xavier Lejeune, Hervé Tostivint, Claire Wyart - Scientific Reports, 2020

Mechanosensory neurons control the timing of spinal microcircuit selection during locomotion. Steven Knafo, Kevin Fidelin, Andrew Prendergast, Po-En Brian Tseng, Alexandre Parrin, Charles Dickey, Urs Lucas Böhm, Sophie Nunes Figueiredo, Olivier Thouvenin, Hugues Pascal-Moussellard, Claire Wyart - Elife, 2017

Zebrazoom: an automated program for high-throughput behavioral analysis and categorization. O Mirat, JR Sternberg, KE Severi, C Wyart - Frontiers in neural circuits, 2013

Feel free to contact us at the address below:


In the unlikely event where the email address above wouldn't work (or if you email us and don't get any response), you can also contact us at: olivier.mirat.om@gmail.com

We welcome all questions and feedback regarding our open-source software ZebraZoom.

We are also available for hire if you need help analyzing animal behavior: see the "Hire Us" section below.

If you like our software, give us a star on Github and follow us on Twitter 😀.