Automated visual tracking for studying the ontogeny of zebrafish swimming

Abstract

SUMMARYThe 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 fishʼs 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. Supplementary material available online at

Visually guided gradation of prey capture movements in larval zebrafish

“…Videos were analyzed using automated tracking software specifically designed to characterize larval zebrafish axial kinematics (Fontaine et al, 2008). The program tracks the outline of the fish using an elastic kinematic model and generates a 51-point midline (Fig.1D).…”

Ontogeny of Swimming Movements in the Catfish Clarias gariepinus

“…Consequently, from 48 hours post-hatching (hPH), the larvae were fed on Artemia salina nauplii 4 to 5 times a day, exclusively during daylight hours. They were haphazardly sampled at 0, 4,8,12,16,20,24,30,36,42,48,60,72,96,120,144,168,192,216,264, and 312 hPH. Adult swimming movements of 5 fish (TL 129 to 156 mm) were also recorded.…”

“…The three main undulatory swimming modes are anguilliform, subcarangiform and carangiform mode. Previous studies dealing with the ontogeny of routine swimming movements in fish have only concerned the carangiform and subcarangiform modes of swimming (carangiform: the cyprinid Danio rerio (Hamilton) [5][6][7][8], the cyprinid Cyprinus carpio L. [9][10][11], the pleuronectid Pleuronectes Platessa L. [12,13]; subcarangiform: the clupeid Clupea harengus L. [14]). To our knowledge, no rigorous study has addressed the ontogeny of anguilliform mode of swimming.…”

Three-dimensional motion tracking reveals a diving component to visual and auditory escape swims in zebrafish larvae

“…In contrast to this, most escape or startle response studies in zebrafish have measured behavior in environments that restrict vertical movement and have tracked swimming two-dimensionally with a single camera above or below the tank. This limitation is apparent in reviews of zebrafish behavioral assays (Budick and O'Malley, 2000;Champagne et al, 2010;Fleisch and Neuhauss, 2006;Mirat et al, 2013) and in tools designed for automated tracking of zebrafish behavior (ZebraLab, ViewPoint;Fontaine et al, 2008). While detailed kinematic information can be obtained from 2D imaging, such as speed, latency, direction and frequency of swimming movements, a restriction in vertical range can be a confound in locomotor assays (Zhu and Weng, 2007) and leaves open the question of whether vertical swimming would occur as part of the 'natural' behavior.…”