Automated visual tracking for studying the ontogeny of zebrafish swimming

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

Automatic Bluefin Tuna sizing using a stereoscopic vision system

[EN] This article presents a non-invasive fully automatic procedure for Bluefin Tuna sizing, based on a stereoscopic vision system and a deformable model of the fish ventral silhouette. An image processing procedure is performed on each video frame to extract individual fish, followed by a fitting proce- dure to adjust the fish model to the extracted targets, adapting it to the bending movements of the fish. The proposed system is able to give accu- rate measurements of tuna snout fork length (SFL) and widths at five predefined silhouette points without manual intervention. In this work, the system is used to study size evolution in adult Atlantic Bluefin Tuna (Thunnus Thynnus) over time in a growing farm. The dataset is composed of 12 pairs of videos, which were acquired once a month in 2015, between July and October, in three grow-out cages of tuna aquaculture facilities on the west Mediterranean coast. Each grow out cage contains between 300 and 650 fish on an approximate volume of 20 000 m3.Measurements were au- tomatically obtained for the 4 consecutive months after caging and suggest a fattening process: SFL shows an increase of just a few centimetres (2%) while themaximum width (A1)shows arelative increaseofmorethan20%,mostlyinthe first 2months in farm. Moreover, a linear relation (with co- efficient of determination R2> 0.98) between SFL and widths for each month is deduced, and a fattening factor (F) is introduced. The validity of the measurements is proved by comparing 15 780 SFL measurements, obtained with our automatic system in the last month, versus ground truth data of a high percentage of the stock under study (1143 out of 1579), obtaining no statistically significant difference. This procedure could be extended to other species to assess the size distribution of stocks, as discussed in the article.This work was supported by funding from ACUSTUNA project ref. CTM2015-70446-R (MINECO/ERDF, EU). This project has been possible thanks to the collaboration of IEO (Spanish Oceanographic Institute).Muñoz-Benavent, P.; Andreu García, G.; Valiente González, JM.; Atienza-Vanacloig, V.; Puig Pons, V.; Espinosa Roselló, V. (2018). Automatic Bluefin Tuna sizing using a stereoscopic vision system. ICES Journal of Marine Science. 75(1):390-401. https://doi.org/10.1093/icesjms/fsx151S39040175

Omnidirectional Sensory and Motor Volumes in Electric Fish

Active sensing organisms, such as bats, dolphins, and weakly electric fish, generate a 3-D space for active sensation by emitting self-generated energy into the environment. For a weakly electric fish, we demonstrate that the electrosensory space for prey detection has an unusual, omnidirectional shape. We compare this sensory volume with the animal's motor volume—the volume swept out by the body over selected time intervals and over the time it takes to come to a stop from typical hunting velocities. We find that the motor volume has a similar omnidirectional shape, which can be attributed to the fish's backward-swimming capabilities and body dynamics. We assessed the electrosensory space for prey detection by analyzing simulated changes in spiking activity of primary electrosensory afferents during empirically measured and synthetic prey capture trials. The animal's motor volume was reconstructed from video recordings of body motion during prey capture behavior. Our results suggest that in weakly electric fish, there is a close connection between the shape of the sensory and motor volumes. We consider three general spatial relationships between 3-D sensory and motor volumes in active and passive-sensing animals, and we examine hypotheses about these relationships in the context of the volumes we quantify for weakly electric fish. We propose that the ratio of the sensory volume to the motor volume provides insight into behavioral control strategies across all animals

Computing the force distribution on the surface of complex, deforming geometries using vortex methods and Brinkman penalization

The distribution of forces on the surface of complex, deforming geometries is an invaluable output of flow simulations. One particular example of such geometries involves self-propelled swimmers. Surface forces can provide significant information about the flow field sensed by the swimmers, and are difficult to obtain experimentally. At the same time, simulations of flow around complex, deforming shapes can be computationally prohibitive when body-fitted grids are used. Alternatively, such simulations may employ penalization techniques. Penalization methods rely on simple Cartesian grids to discretize the governing equations, which are enhanced by a penalty term to account for the boundary conditions. They have been shown to provide a robust estimation of mean quantities, such as drag and propulsion velocity, but the computation of surface force distribution remains a challenge. We present a method for determining flow- induced forces on the surface of both rigid and deforming bodies, in simulations using re-meshed vortex methods and Brinkman penalization. The pressure field is recovered from the velocity by solving a Poisson's equation using the Green's function approach, augmented with a fast multipole expansion and a tree- code algorithm. The viscous forces are determined by evaluating the strain-rate tensor on the surface of deforming bodies, and on a 'lifted' surface in simulations involving rigid objects. We present results for benchmark flows demonstrating that we can obtain an accurate distribution of flow-induced surface-forces. The capabilities of our method are demonstrated using simulations of self-propelled swimmers, where we obtain the pressure and shear distribution on their deforming surfaces

Emerging technologies for reef fisheries research and management [held during the 56th annual Gulf and Caribbean Fisheries Institute meeting in Tortola, British Virgin Islands, November 2003]

This publication of the NOAA Professional Paper NMFS Series is the product of a special symposium on “Emerging Technologies for Reef Fisheries Research and Management” held during the 56th annual Gulf and Caribbean Fisheries Institute meeting in Tortola, British Virgin Islands, November 2003. The purpose of this collection is to highlight the diversity of questions and issues in reef fisheries management that are benefiting from applications of technology. Topics cover a wide variety of questions and issues from the study of individual behavior, distribution and abundance of groups and populations, and associations between habitats and fish and shellfish species.(PDF files contains 124 pages.

Enhanced fish bending model for automatic tuna sizing using computer vision

[EN] This paper presents a non-invasive fully automatic procedure to obtain highly accurate fish length estimation in adult Bluefin Tuna, based on a stereoscopic vision system and a deformable model of the fish ventral silhouette. The present work takes a geometric tuna model, which was previously developed by the same authors to discriminate fish in 2D images, and proposes new models to enhance the capabilities of the automatic procedure, from fish discrimination to accurate 3D length estimation. Fish length information is an important indicator of the health of wild fish stocks and for predicting biomass using length-weight relations. The proposal pays special attention to parts of the fish silhouette that have special relevance for accurate length estimation. The models have been designed to best fit the rear part of the fish, in particular the caudal peduncle, and a width parameter has been added to better fit the silhouette. Moreover, algorithms have been developed to extract snout tip and caudal peduncle features, allowing better initialization of model parameters. Snout Fork Length (SFL) measurements using the different models are extracted from images recorded with a stereoscopic vision system in a sea cage containing 312 adult Atlantic Bluefin Tuna. The automatic measurements are compared with two ground truths: one configured with semiautomatic measurements of favourable selected samples and one with real SFL measurements of the tuna stock collected at harvesting. Comparison with the semiautomatic measurements demonstrates that the combination of improved geometric models and feature extraction algorithms delivers good results in terms of fish length estimation error (up to 90% of the samples bounded in a 3% error margin) and number of automatic measurements (up to 950 samples out of 1000). When compared with real SFL measurements of the tuna stock, the system provides a high number of automatic detections (up to 6706 in a video of 135¿min duration, i.e., 50 automatic measurements per minute of recording) and highly accurate length measurements, obtaining no statistically significant difference between automatic and real SFL frequency distributions. This procedure could be extended to other species to assess the size distribution of stocks, as discussed in the paper.This work was supported by funding from ACUSTUNA project ref. CTM2015-70446-R (MINECO/ERDF, EU). This project has been possible thanks to the collaboration of IEO (Spanish Oceanographic Institute). We acknowledge the assistance provided by the Spanish company Grup Balfego S.L. in supplying boats and divers to acquire underwater video in the Mediterranean Sea.Muñoz-Benavent, P.; Andreu García, G.; Valiente González, JM.; Atienza-Vanacloig, V.; Puig Pons, V.; Espinosa Roselló, V. (2018). Enhanced fish bending model for automatic tuna sizing using computer vision. Computers and Electronics in Agriculture. 150:52-61. https://doi.org/10.1016/j.compag.2018.04.005S526115

Multibeam volume acoustic backscatter imagery and reverberation measurements in the Northeastern Gulf of Mexico

Multibeam volume acoustic backscatterimagery and reverberation measurements are derived from data collected in 200-m-deep waters in the northeastern Gulf of Mexico, with the Toroidal Volume Search Sonar (TVSS), a 68-kHz cylindrical sonar operated by the U.S. Navy’s Coastal System Station. The TVSS’s 360-degree vertical imaging plane allows simultaneous identification of multiple volume scattering sources and their discrimination from backscatter at the sea surface or the seafloor. This imaging capability is used to construct a three-dimensional representation of a pelagic fish school near the bottom. Scattering layers imaged in the mixed layer and upper thermocline are attributed to assemblages of epipelagic zooplankton. The fine scale patchiness of these scatterers is assessed with the two-dimensional variance spectra of vertical volume scattering strength images in the upper and middle water column. Mean volume reverberation levels exhibit a vertical directionality which is attributed to the volume scattering layers. Boundary echo sidelobe interference and reverberation is shown to be the major limitation in obtaining bioacoustic data with the TVSS. Because net tow and trawl samples were not collected with the acoustic data, the analysis presented is based upon comparison to previous biologic surveys in the northeastern Gulf of Mexico and reference to the bioacoustic literature

Simulação numérica 3D do escoamento em escadas para peixes com ranhura vertical : validação do modelo e caracterização do escoamento

Vertical slot fishways allow energy dissipation as a function of the pool, longitudinal slope, baffle and vertical slot design. The mean and turbulent flow patterns in these structures must be compatible with the fish target. The design of these structures is commonly based on previous successful fishways as well as simplified theoretical equations and empirical relationships. To aid in the design of these structures, a three-dimensional hydrodynamic model was used to simulate the flow, and experimental studies were used to validate the model. The mean velocities, pressures and parameters indicative of turbulence were analyzed. The maximum flow velocities were up to 32% higher than the values obtained using a simplified theoretical equation. The evaluation of the volumetric dissipated power indicated that the mean value for the pool was lower than 150 W/m3; however, analysis of the spatial distribution showed that in some areas, the values can exceed 1000 W/m3. The results indicate that the numerical simulation was able to adequately represent the flow considering the computational cost involved. Accordingly, it can be used as a complementary tool for the design of new fishways and for the analysis of modifications in existing ones.As escadas para peixes com ranhuras verticais permitem que ocorra a dissipação da energia do escoamento em função da forma da bacia, dos defletores, da declividade longitudinal e da largura da ranhura vertical. Estas estruturas devem apresentar padrões médios e turbulentos do escoamento compatíveis com os peixes que irão transpô-la. Tipicamente a concepção das escadas para peixes é baseada na utilização de geometrias empregadas com sucesso em situações anteriores e a estimativa das características do escoamento através de equações teóricas simplificadas e relações empíricas. Para contribuir na concepção dessas estruturas, foi utilizado um modelo hidrodinâmico tridimensional para simular o escoamento e estudos experimentais para validar o modelo. Velocidades médias, pressões e parâmetros indicativos da turbulência foram analisados. As velocidades máximas do escoamento foram até 32% superiores aos valores obtidos utilizando uma equação teórica simplificada. A avaliação da potência dissipada por unidade de volume indica que o valor médio para o tanque é inferior a 150 W/m3, no entanto, a análise da distribuição espacial desta grandeza no tanque, mostra que valores pontuais podem ultrapassar 1000 W/m3. Os resultados indicam que a simulação numérica foi capaz de representar de forma adequada o escoamento, considerando o custo computacional envolvido e pode ser utilizada como uma ferramenta complementar para o projeto de novas escadas para peixes e para a análise de modificações em estruturas existentes

Automatic Bluefin Tuna (Thunnus thynnus) Biomass Estimation during Transfers Using Acoustic and Computer Vision Techniques

In this work, acoustic and computer vision techniques are combined to develop an automatic procedure for biomass estimation of tuna during transfers. A side scan sonar working at 200 kHz and a stereo camera, posi- tioned facing towards the surface to record the ventral aspect of fish, are set as acquisition equipment. Moreover, a floating structure has been devised to place the sensors between cages in transfers, creating a transfer canal that allows data acquisition while fish swim from donor to receiving cage. Biomass assessment is computed by counting transferred tuna and sizing a representative sample of the stock. The number of transferred tuna is automatically deduced from acoustic echograms by means of image processing techniques, whereas tuna size is computed from the stereo videos using our automatic computer vision procedure based on a deformable model of the fish ventral silhouette. The results show that the system achieves automatic tuna counting with error below 10%, achieving around 1% error in the best configuration, and automatic tuna sizing of more than 20% of the stock, with highly accurate Snout Fork Length estimation when compared to true data from harvests. These results fulfil the requirements imposed by International Commission for the Conservation of Atlantic Tunas for compliant transfer operations.Versión del editor1,42