Ensembles of wrappers for automated feature selection in fish age classification

In feature selection, the most important features must be chosen so as to decrease the number thereof while retaining their discriminatory information. Within this context, a novel feature selection method based on an ensemble of wrappers is proposed and applied for automatically select features in fish age classification. The effectiveness of this procedure using an Atlantic cod database has been tested for different powerful statistical learning classifiers. The subsets based on few features selected, e.g. otolith weight and fish weight, are particularly noticeable given current biological findings and practices in fishery research and the classification results obtained with them outperforms those of previous studies in which a manual feature selection was performed.Peer ReviewedPostprint (author's final draft

Semi-local extraction of ring structures in images of biological hard tissues: application to the Bayesian interpretation of fish otoliths for age and growth estimation

International audienceThis paper deals with the analysis of images of biological tissue that involves ring structures, such as tree trunks, bivalve seashells or fish otoliths, with a view to automating the acquisition of age and growth data. A bottom-up template-based scheme extracts meaningfulridge and valley curve data using growth-adapted time-frequency filtering. Age and growth estimation is then stated as the Bayesian selection of a subset of ring curves, combining ameasure of curve significativity and ana prioristatistical growth model. Experiments on realsamples demonstrate the efficiency of the proposed extraction stage. Our Bayesian frameworkis shown to significantly outperform previous methods for the interpretation of a dataset of200 plaice otoliths and compares favorably to inter-expert agreement rates (88% of agreement to expert interpretations)

Automated fish age estimation from otolith images using statistical learning

International audienceThe acquisition of age and growth data is of key importance for fisheries research (assessment, marine ecology issues, etc.). Consequently, automating this task is of great interest. In this paper, we investigate the use of statistical learning techniques for fish age estimation. The core of this study lies in the definition of relevant image-related features. We rely on the computation of a 1D representation summing up the content of otolith images within a predefined area of interest. Features are then extracted from this non-stationary representation depicting the alternation of seasonal growth rings. Thus, fish age estimation can be viewed as a multi-class classification issue using statistical learning strategies. In particular, a procedure based on demodulation and remodulation of fish growth patterns is used to improve the generalization properties of the trained classifiers. The experimental evaluation is carried out over a dataset of 320 plaice otolith images from age groups 1–6. We analyze both, the performances of several statistical classifiers, namely SVMs (support vector machines) and neural networks, and the relevance of the proposed image-based feature sets. In addition, the combination of additional biological and shape features to the image-related ones is considered. We reach a rate of correct age estimation of 88% w.r.t. the expert ground truth. This demonstrates the relevance of the proposed approach for the automation of routine aging and for computer-assisted aging

AGE, GROWTH, AND OTOLITH MICROCHEMISTRY OF GOLDEN TILEFISH (LOPHOLATILUS CHAMAELEONTICEPS) IN THE NW ATLANTIC

Knowledge of life-history characteristics and patterns of connectivity are important parameters to fisheries management, especially for species inhabiting hard to reach environments, such as the deep-sea. Golden Tilefish (Lopholatilus chamaeleonticeps) are slow growing, long-lived, demersal species that exhibit a patchy distribution along the continental shelf-edge of the NW Atlantic Ocean. Golden Tilefish create burrows in the clay sediment and maintain high site fidelity. These characteristics suggest the possibility of localized subpopulations across the species’ distribution; an important consideration for the resilience of this species to fishing pressure. My objectives are (1) to estimate age, and model growth of fish captured from a fishery-independent survey and compare these estimates to assessments derived from fishery-dependent data, and (2) to investigate temporal and spatial patterns of habitat connectivity using otolith elemental signatures as natural tags that discriminate subpopulations. Age and growth estimates were consistent consistency with previous assessments and provided an unbiased analysis of the population that can be used for further monitoring. Analysis of elemental profiles indicated subtle spatial differences, suggesting the application for delineating subpopulations. Elemental profiles also varied between years and may represent differing environmental characteristics experienced by the individuals during their pelagic larval stage and subsequent settlement. My thesis contributes age, growth and population connectivity data that will aid in monitoring the stock and development of management decision

Metapopulation dynamics of the softshell clam, Mya arenaria

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2008In this dissertation, I explored metapopulation dynamics and population connectivity, with a focus on the softshell clam, Mya arenaria. I first worked towards developing a method for using elemental signatures retained in the larval shell as a tag of natal habitat. I designed and implemented an experiment to determine whether existing methods commonly used for fishes would be applicable to bivalves. I found that the instrumentation and setup I used were not able to isolate and measure the first larval shell of M. arenaria. In concert with developing this method for bivalves, I reared larval M. arenaria in the laboratory under controlled conditions to understand the environmental and biological factors that may influence elemental signatures in shell. My results show that growth rate and age have significant effects on juvenile shell composition, and that temperature and salinity affect larval and juvenile shell composition in variable ways depending on the element evaluated. I also examined the regional patterns of diversity over the current distribution of M. arenaria using the mitochondrial gene, cytochrome oxidase I (COI). I found minimal variability across all populations sampled, suggesting a recent population expansion in the Northwest Atlantic. Finally, I employed theoretical approaches to understand patch dynamics in a two-patch metapopulation when one patch is of high quality and the other low quality. I developed a matrix metapopulation model and compared growth rate elasticity to patch parameters under variable migration scenarios. I then expanded the model to include stochastic disturbance. I found that in many cases, the spatial distribution of individuals within the metapopulation affects whether growth rate is most elastic to parameters in the good or bad patch.Financial support was provided by the National Defense Science and Engineer- ing Graduate Fellowship; the WHOI Academic Programs O±ce; NSF grants OCE- 0326734, OCE-0215905, OCE-0349177, DEB-0235692, DMS-0532378, and ATM-0428122; and by NOAA National Sea Grant College Program O±ce, Department of Commerce, under Grant No. NA86RG0075 (Woods Hole Oceanographic Institution Sea Grant Project No. R/0-32), and Grant No. NA16RG2273 (WHOI Sea Grant Project No. R/0-35)

Structure and growth of Pacific halibut otoliths: Identifying spatial and temporal variation

Thesis (Ph.D.) University of Alaska Fairbanks, 1997Otoliths are polycrystals of calcium carbonate and protein that grow through the process of biomineralization within the otic capsule of teleost fish. Otoliths of Pacific halibut (Hippoglossus stenolepis) are routinely collected to provide age information, but other information has not been examined in detail. The purpose of this study was to investigate whether otolith structural patterns reveal information about otolith growth, and by inference, about fish growth and habitat during its early life. Variation in the increment widths of the first five annuli of adult halibut otoliths over a 26 year period were partitioned in two ways: the year the growth took place and the year-class to which the fish belonged. The year of growth explained temporal variation in the youngest ages and was attributed to changes in temperature which may influence recruitment success, while the year-class of growth explained temporal variation in older juveniles, but could reflect sampling bias. An analysis of microstructure increments indicated that relative otolith growth rate was an indicator of larval somatic growth. Young halibut from the Gulf of Alaska exhibited similar larval growth histories, though individual and nursery area differences were apparent. Specimens from the Bering Sea had slower larval growth rates than halibut from the Gulf of Alaska. Trace levels of strontium within otoliths were associated with ontogenetic changes of larvae and winter annuli formation of adults. Levels of potassium and sodium varied by nursery area of capture suggesting some utility for stock separation, though there was indication of significant interannual variation. The shape of the larval crystal within the otolith microstructure of young halibut was found not to be associated with nursery area of capture, and thus is not a good candidate as a stock separation tool. The high variation within individuals suggests that the shape of the crystal is not determined by external events. Overall, several patterns preserved in otoliths can provide insight into processes that influence the growth of halibut and distribution of individuals and these patterns can be recovered from adult fish. However careful interpretation is still required to separate meaningful information from spurious data

Growth ring detection and modelling on otolith images by demodulation and graph construction

In a resource rarefaction context, developing reliable systems for stocks characterization is of key importance for marine ecosystems management. Otoliths, calcified structures located in the inner ear of the fishes, are classically used to acquire data on age and growth of an individual. This paper deals with the problem of design and realization of a computer vision system for the recognition of patterns on otolith images. The principal problem we will be interested in is the invariance of the local operators facing structures with multi-scale nature (as in otolith images). We propose a solution which consists in demodulating the image in order to eliminate the non-linearity of the ring size, given a priori knowledge on the law governing the growth of these structures. The result of this work is an alternative of segmentation by graph construction, based on the general principles of perceptive grouping. In addition, we undertake studies of validations of the proposed solution on a reference test image set (N = 102) of plaice otoliths, previously aged by one reader. We show the interest of this solution for calcified structure reading while establishing a comparison between our results and those coming from previously developed 1D-approach detection or template-approach one.Dans un contexte de raréfaction de la ressource, le développement de systèmes fiables pour la caractérisation des stocks halieutiques est un enjeu majeur pour la gestion durable des écosystèmes marins. Les otolithes, pièces calcifiées situées au niveau de l’oreille interne des poissons, sont classiquement utilisées comme des chronomètres permettant l’estimation de l’âge et de la croissance d’un individu. Cet article traite du problème de la mise au point d’un système permettant l’extraction automatique d’information dans les images d’otolithes par vision artificielle. Nous nous intéressons plus particulièrement au problème de l’invariance des opérateurs locaux de prétraitement et de segmentation, face à des structures de nature multi-échelle dans les images d’otolithes. La solution au concept simple que nous proposons consiste à démoduler l’image en vue de soustraire la non-linéarité de la largeur des accroissements, étant donnée une estimation de la loi régissant la croissance de ces structures. Egalement, nous développons une nouvelle technique de segmentation de ces images, technique qui opère dans un espace transformé et qui est basée sur les principes généraux de groupement perceptif empruntés de la théorie Gestaltiste. À partir d’un même échantillon témoin de 102 images d’otolithes de Plies, nous comparons par la suite l’efficacité de cette technique à celle d’une approche de détection monodimensionnelle, et à celle du modèle « template qualitatif » précédemment développé. La quantification des résultats obtenus laisse voir une certaine supériorité des performances obtenues avec cette approche de segmentation par démodulation et construction de graphe

BIO-ECOLOGICAL AND ANATOMICAL ASPECTS OF THE EUROPEAN EEL ANGUILLA ANGUILLA (L. 1758)

Catadromous fish are considered important species for their ecological, economical, and cultural value. Because their complex life cycle, they are subjected to cumulative effects of anthropogenic threats that resulted in worldwide decline since the beginning of the 20th century. Among the most iconic catadromous species, the European eel Anguilla anguilla (L.) has aroused considerable interest since ancient times, though, to date, many aspects of its life cycle remain relatively unknown. A. anguilla showed a progressively decline since the 1970s. Starting from 2007, has been protected by the European Council Regulation 1100/2007, and successively classified as Critically Endangered (CR). Although conspicuous efforts have been conducted, to implement knowledge and identify possible solutions to preserve the future survivorship of A. anguilla, there is an urgent need to gain further insights into its life history. A review of the bibliography allowed me to obtain an updated state of the art of knowledge about the European eel life cycle, biology, ecology, allowing me to identify main topics that structured my thesis project. Topics have been developed with the general aim of providing a contribution to the implementation of the knowledge of the bio-ecology and anatomy of this species in relation to the various environmental and anthropic factors through a multidisciplinary approach that involved numerous sampling activities accompanied by complex data collection, laboratory experiments, and statistical analyses. First, I demonstrated the presence of synaptic development in the olfactory bulb, in terms of morphology and density of dendritic spines, that is shaped according to a pattern linked to the migratory life stages of the European eel (glass eels and silver eels). Second, I described the glass eels’ migration temporal peak for the first time in the central-western Mediterranean in relation to the effects of main environmental factors. I also identified a spatio-temporal variability between four sites in the western Mediterranean in terms of the peak of recruitment and the biometric and pigmentation patterns of glass eels. Moreover, I tested new floating traps as an alternative sampling method in three Sardinian estuaries to further deepen glass eels’ recruitment dynamics in Sardinia. Third, I analysed eels’ survival and growth performances during a rearing experiment with wild glass eels. I estimated recapture and growth rates on marked and unmarked farmed eels after restocking after a four-year study. Results suggest a good readjustment to the wild environment and demonstrated that this technique could represents a valid alternative restocking approach. Furthermore, I studied eels’ growth also in terms of otoliths’ shape differences. I found a distinct clustering among rivers and lagoons, with more rounded otoliths shapes in eels from rivers than lagoons, but with annual body growth quicker in lagoons than in rivers, showing that eel’s growth can differ according to habitat types. I fitted Von Bertalanffy’s growth curves for female and male eels from a Sardinian stream, that exhibited the already-known sexual dimorphism in growth parameters with higher values in females. Finally, I pinpointed an overall decrease in eels’ occurrence in the Sardinian river network because of dams’ building features and the time from their construction. Achieved results might have several implications beyond the regional interest and add new points from which to start further investigations that, over specific actions, may guide the implementation of new studies and appropriate monitoring programs. Findings highlighted also an urgent need for collaboration between the various stakeholders, researchers, decision-makers, authorities, professionals, and common people as an essential step to creating a sense of awareness on the criticalities that impact this species and the need to mitigate them

Recrystallization of Biogenic Aragonite Shells from Archaeological Contexts and Implications for Paleoenvironmental Reconstruction

Archaeologists do not consistently test the mineralogy of archaeological bivalve shells before conducting isotope analysis for paleoenvironmental reconstruction. This is a problem because if biogenic aragonite is heated, or cooked, it can recrystallize into calcite, and can become depleted of its heavy oxygen and carbon isotopes. Oxygen isotope ratios are recorded in the growth rings of bivalve shells as they grow, and reflect the temperature conditions of the ambient ocean water. Thus, ancient bivalve shells are used to reconstruct paleoenvironments. I have conducted an experiment to demonstrate the importance of testing the mineralogy of archaeological shells before isotope analysis. I collected modern specimens of four different bivalve taxa and separated them into left and right valves. I heated the left valves in an oven at three controlled temperatures, and I retained the right valves as unheated controls. I conducted mineralogy and isotope analysis on all valves and compared the left and rights of each individual. I found that valves heated to about 400˚C for one hour had recrystallized into calcite and had significantly altered oxygen isotope ratios. This happened before the shell appeared charred. I also conducted mineralogy testing on seven archaeological shell fragments from the Tse-Whit-Zen Village Site (45CA523). Of the seven archaeological specimens, one was entirely calcite, and two had traces of calcite in them. The two fragments containing minor amounts of calcite did not show any visible signs that they were altered or otherwise different from fragments that were entirely aragonite. It is unlikely that archaeologists will know if shells are heated unless mineralogy testing is conducted