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Automated visual tracking for studying the ontogeny of zebrafish swimming

Fontaine, Ebraheem and Lentink, David and Kranenbarg, Sander and Müller, Ulrike K. and van Leeuwen, Johan L. and Barr, Alan H. and Burdick, Joel W. (2008) Automated visual tracking for studying the ontogeny of zebrafish swimming. Journal of Experimental Biology, 211 (8). pp. 1305-1316. ISSN 0022-0949. https://resolver.caltech.edu/CaltechAUTHORS:FONjeb08

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PDF (Fig. S1. Example of center of volume (COV) and center of area (COA) calculation for zebrafish at age 5 days) - Supplemental Material
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PDF (Fig. S2. Example of center of volume (COV) and center of area (COA) calculation for zebrafish at age 15 days) - Supplemental Material
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PDF (Fig. S3. Example of center of volume (COV) and center of area (COA) calculation for zebrafish at age 28 days) - Supplemental Material
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PDF (Fig. S4. Location of center of volume (COV) and center of area (COA) measured posterior from the snout of the fish. For ages 5, 15 and 28 days, we measured data from 3, 5 and 4 fish, respectively) - Supplemental Material
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[img] Video (QuickTime) (Movie 1. 15 d.p.f. wild-type zebrafish. Tracking results for 15 d.p.f. wild-type zebrafish) - Supplemental Material
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Abstract

The zebrafish Danio rerio is a widely used model organism in studies of genetics, developmental biology, and recently, biomechanics. In order to quantify changes in swimming during all stages of development, we have developed a visual tracking system that estimates the posture of fish. Our current approach assumes planar motion of the fish, given image sequences taken from a top view. An accurate geometric fish model is automatically designed and fit to the images at each time frame. Our approach works across a range of fish shapes and sizes and is therefore well suited for studying the ontogeny of fish swimming, while also being robust to common environmental occlusions. Our current analysis focuses on measuring the influence of vertebra development on the swimming capabilities of zebrafish. We examine wild-type zebrafish and mutants with stiff vertebrae (stocksteif) and quantify their body kinematics as a function of their development from larvae to adult (mutants made available by the Hubrecht laboratory, The Netherlands). By tracking the fish, we are able to measure the curvature and net acceleration along the body that result from the fish's body wave. Here, we demonstrate the capabilities of the tracking system for the escape response of wild-type zebrafish and stocksteif mutant zebrafish. The response was filmed with a digital high-speed camera at 1500 frames s–1. Our approach enables biomechanists and ethologists to process much larger datasets than possible at present. Our automated tracking scheme can therefore accelerate insight in the swimming behavior of many species of (developing) fish.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1242/jeb.010272DOIUNSPECIFIED
http://jeb.biologists.org/cgi/content/abstract/211/8/1305PublisherUNSPECIFIED
Additional Information:© The Company of Biologists Ltd 2008. Accepted 21 February 2008. First published online March 28, 2008. The authors would like to thank B. Walderich, H. M. Maischein and J. Odenthal of the Hubrecht laboratory for graciously allowing us to use video of the stocksteif mutant for demonstrating the ability of our tracker system. We also thank Ansa Wasim for recording the movie sequences and Henk Schipper for capturing the photographs used in the COV calculations. E.I.F., A.H.B. and J.W.B. thank the Beckman Institute of Caltech for providing financial support of this project. D.L. and J.L.v.L. are funded by NOW-ALW grant 817.02.012. Supplementary material available online at http://jeb.biologists.org/cgi/content/full/211/8/1305/DC1
Funders:
Funding AgencyGrant Number
Beckman Institute, CaltechUNSPECIFIED
Netherlands Organization for Scientific Research817.02.012
Subject Keywords:tracking, geometric modeling, estimation, zebrafish, swimming
Issue or Number:8
Record Number:CaltechAUTHORS:FONjeb08
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:FONjeb08
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:12737
Collection:CaltechAUTHORS
Deposited By: Archive Administrator
Deposited On:22 Dec 2008 17:18
Last Modified:03 Oct 2019 00:31

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