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A HMM-based model to geolocate pelagic fish from high-resolution individual temperature and depth histories: European sea bass as a case study ArchiMer
Woillez, Mathieu; Fablet, Ronan; Tran-thanh Ngo,; Lalire, Maxime; Lazure, Pascal; De Pontual, Helene.
Numerous methods have been developed to geolocate fish from data storage tags. Whereas demersal species have been tracked using tide-driven geolocation models, pelagic species which undertake extensive migrations have been mainly tracked using light-based models. Here, we present a new HMM-based model that infers pelagic fish positions from the sole use of high-resolution temperature and depth histories. A key contribution of our framework lies in model parameter inference (diffusion coefficient and noise parameters with respect to the reference geophysical fields—satellite SST and temperatures derived from the MARS3D hydrodynamic model), which improves model robustness. As a case study, we consider long time series of data storage tags (DSTs) deployed on...
Tipo: Text Palavras-chave: Fish movement; Archival tagging; Migration; Population structure; Hidden Markov Model (HMM); State-space model.
Ano: 2016 URL: http://archimer.ifremer.fr/doc/00300/41097/40270.pdf
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A review of image-based tools for automatic fish ageing from otolith features ArchiMer
Carbini, Sebastien; Chessel, Anatole; Benzinou, Abdesslam; Fablet, Ronan; Mahe, Kelig; De Pontual, Helene.
Most of European fish stocks are assessed using age-based models, and otolith interpretation for age estimations costs several million euros annually. In this context, automated ageing systems would provide a mean to 1) standardize ageing, 2) control ageing consistency within and between ageing laboratories 3) build interpreted image data bases ensuring the information conservation and sharing and 4) improve growth studies while reducing the cost of the acquisition of age data. This paper presents a review of different image-based tools for automatic fish ageing from otolith features within the framework of AFISA (EU STREP project on Automated FISh Ageing coordinated by Ifremer). The full automatic ageing process can be divided into three main steps: 1)...
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Ano: 2008 URL: http://archimer.ifremer.fr/doc/00024/13519/10546.pdf
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Are hake otolith macrostructures randomly deposited? Insights from an unsupervised statistical and quantitative approach applied to Mediterranean hake otoliths ArchiMer
Courbin, Nicolas; Fablet, Ronan; Mellon-duval, Capucine; De Pontual, Helene.
Individual fish age data are crucial to fish stock assessment, so their accuracy and precision are vital. The acquisition of age data most often relies on interpreting fish otoliths, a complex task in which expert subjectivity increases with the complexity of the structural patterns of the otoliths. The question arises for certain fish species (e.g. hake, Merluccius merluccius) whether the deposition of otolith macrostructures is meaningful for age estimation. A quantitative method based on the evaluation of otolith similarity in terms of structural patterns is presented to investigate this issue. It relies on the determination of a typology of otolith macrostructures from an unsupervised statistical analysis of the distributions of their characteristics....
Tipo: Text Palavras-chave: Quality control; Otolith; Merluccius merluccius; Growth; Age estimation method; Age.
Ano: 2007 URL: http://archimer.ifremer.fr/doc/2007/publication-2678.pdf
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Automatic Fish Ageing (AFISA) ArchiMer
Mahe, Kelig; Parisi, Vincenc; Carbini, Sebastien; Soria, J.a.; Harbitz, A; De Pontual, Helene; Cotano, U; Songer, S; Millner, R; Lewy, P; Gudmundsson, E.f; Fablet, Ronan; Benzinou, Abdesslam.
Most of the fish stocks are assessed using age-based models, however age estimations using otoliths costs several million euros annually. In this context, Automatic Fish Ageing (EU Project) would provide means to standardize ageing among laboratories and build interpreted image databases ensuring the information conservation. Automation improves growth studies while reducing the cost of the acquisition of age data. The whole processing chain from the acquisition of otolith data to the actual ageing issue using pattern recognition or statistical inference has been realised for three case studies : a) Cod (Gadus morhua ; Faeroes, North Sea, North East Arctic) b) Anchovy (Engraulis encrasicolus ; Bay of Biscay) c) Plaice (Pleuronectes platessa, Eastern...
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Ano: 2009 URL: http://archimer.ifremer.fr/doc/00011/12270/10548.pdf
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Automatic morphological detection of otolith nucleus ArchiMer
Cao, Frédéric; Fablet, Ronan.
This paper deals with the automation of the acquisition of age and growth data from the analysis of otolith images. One of the key component of such it system is the automatic detection of the growth center, which serves as the basis for further processing (2D ring segmentation, age and growth estimation,...). To this end, we develop a new and well-founded approach combining a morphological analysis of image level sets to the a contrario, detection principle. This approach leads to a robust parameterless scheme, whose efficiency is demonstrated by an evaluation carried out for a set of several hundred of plaice otoliths. (c) 2005 Elsevier B.V. All rights reserved.
Tipo: Text Palavras-chave: Otolith imaging; A contrario detection; Mathematical morphology.
Ano: 2006 URL: http://archimer.ifremer.fr/doc/2006/publication-1223.pdf
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Brève introduction à la fouille de grandes bases de données océaniques ArchiMer
Maze, Guillaume; Mercier, Herle; Fablet, Ronan; Lenca, Philippe; Piolle, Jean-francois.
Les bases de données marines, alimentées par les satellites et les robots autonomes sous-marins comme les flotteurs du réseau Argo, sont de plus en plus grandes (plusieurs dizaines de gigaoctets et teraoctets) et rapidement évolutives (elles changent d’heure en heure). Cette augmentation spectaculaire de la dimension et de la complexité des données rend difficile leur exploitation avec les outils standards. Or, c’est à partir de l’analyse des données que les chercheurs pourront réaliser de nouvelles découvertes scientifiques sur la dynamique des océans, à grande et petite échelles, et les changements climatiques régionaux et globaux. L'école d’été OBIDAM14 visait à contribuer à lever ces verrous d’analyse en introduisant les méthodes de fouille de données...
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Ano: 2014 URL: http://archimer.ifremer.fr/doc/00216/32710/31075.pdf
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Coherent heat patterns revealed by unsupervised classification of Argo temperature profiles in the North Atlantic Ocean ArchiMer
Maze, Guillaume; Mercier, Herle; Fablet, Ronan; Tandeo, Pierre; Radcenco, Manuel Lopez; Lenca, Philippe; Feucher, Charlene; Le Goff, Clement.
A quantitative understanding of the integrated ocean heat content depends on our ability to determine how heat is distributed in the ocean and what are the associated coherent patterns. This study demonstrates how this can be achieved using unsupervised classification of Argo temperature profiles. The classification method used is a Gaussian Mixture Model (GMM) that decomposes the Probability Density Function of a dataset into a weighted sum of Gaussian modes. It is determined that the North Atlantic Argo dataset of temperature profiles con- tains 8 groups of vertically coherent heat patterns, or classes. Each of the temperature profile classes reveals unique and physically coherent heat distributions along the vertical axis. A key result of this study is...
Tipo: Text Palavras-chave: Heat content; Classification North Atlantic; Stratification; Water mass; Thermocline; Argo; Pattern.
Ano: 2017 URL: http://archimer.ifremer.fr/doc/00363/47431/47456.pdf
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Computer vision and otolith: toward a modelisation of the morphogenesis ofaccretionary processes ArchiMer
Chessel, Anatole; Fablet, Ronan; Cao, Frederic.

Otolith are small stone growing according to an accretionary process located in fishes inner ears from which a lot can be learnt about their biology and ecology. Computer vision is one of the mean of systematic analysis of those stone. This paper describe an approach using partial differential equation and variational methods to reconstruct the morphogenesis of an otolith from an image.

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Ano: 2008 URL: https://archimer.ifremer.fr/doc/00479/59096/61734.pdf
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Coupling spectral analysis and hidden Markov models for the segmentation of behavioural patterns ArchiMer
Heerah, Karine; Woillez, Mathieu; Fablet, Ronan; Garren, Francois; Martin, Stephane; De Pontual, Helene.
Background Movement pattern variations are reflective of behavioural switches, likely associated with different life history traits in response to the animals’ abiotic and biotic environment. Detecting these can provide rich information on the underlying processes driving animal movement patterns. However, extracting these signals from movement time series, requires tools that objectively extract, describe and quantify these behaviours. The inference of behavioural modes from movement patterns has been mainly addressed through hidden Markov models. Until now, the metrics implemented in these models did not allow to characterize cyclic patterns directly from the raw time series. To address these challenges, we developed an approach to i) extract new metrics...
Tipo: Text Palavras-chave: Fourier transform; Non negative matrix factorization; Classification; Animal behaviour; European sea bass; Movement ecology; Diurnal and tidal cycles; Biologging; Data storage tags.
Ano: 2017 URL: https://archimer.ifremer.fr/doc/00402/51400/51974.pdf
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Data-driven assimilation of irregularly-sampled image time series ArchiMer
Fablet, Ronan; Viet, P.; Lguensat, R.; Chapron, Bertrand.
We address in this paper the reconstruction of irregurlarlysampled image time series with an emphasis on geophysical remote sensing data. We develop a data-driven approach, referred to as an analog assimilation and stated as an ensemble Kalman method. Contrary to model-driven assimilation models, we do not exploit a physically-derived dynamic prior but we build a data-driven dynamic prior from a representative dataset of the considered image dynamics. Our contribution is here to extend analog assimilation to images, which involve high-dimensional state space.We combine patch-based representations to a multiscale PCA-constrained decomposition. Numerical experiments for the interpolation of missing data in satellite-derived ocean remote sensing images...
Tipo: Text Palavras-chave: Data assimilation; Irregular sampling; Image time series; Data-driven methods; Kalman methods.
Ano: 2017 URL: https://archimer.ifremer.fr/doc/00403/51440/52009.pdf
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Data-Driven Interpolation of Sea Level Anomalies Using Analog Data Assimilation ArchiMer
Lguensat, Redouane; Viet, Phi Huynh; Sun, Miao; Chen, Ge; Fenglin, Tian; Chapron, Bertrand; Fablet, Ronan.
From the recent developments of data-driven methods as a means to better exploit large-scale observation, simulation and reanalysis datasets for solving inverse problems, this study addresses the improvement of the reconstruction of higher-resolution Sea Level Anomaly (SLA) fields using analog strategies. This reconstruction is stated as an analog data assimilation issue, where the analog models rely on patch-based and Empirical Orthogonal Functions (EOF)-based representations to circumvent the curse of dimensionality. We implement an Observation System Simulation Experiment (OSSE) in the South China Sea. The reported results show the relevance of the proposed framework with a significant gain in terms of Root Mean Square Error (RMSE) for scales below 100...
Tipo: Text Palavras-chave: Analog data assimilation; Sea level anomaly; Sea surface height; Interpolation; Data-driven methods.
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00489/60078/63402.pdf
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Des otolithes aux satellites: méthodes et applications du traitement du signal et des images pour l'observation de l'océan ArchiMer
Fablet, Ronan.
This document presents a synthesis of my research activities over the last 10 years initially within the Ifremer-IRD schlerochronology laboratory and the Fisheries Science and Technology department at Ifremer, and then at the Signal & Communication Department of Telecom Bretagne. My research activities were undertaken at the interface of Information Science and Technology and Oceanography. In the framework of interdisciplinary approaches, my research work addressed the development of new image and signal processing tools and methods with a view to (1) providing new representations of the obsvered scenes or processes, (2) exploiting these representations to infer or reconstruct patterns of interest for the considered thematic objectives. Three thematic...
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Ano: 2012 URL: http://archimer.ifremer.fr/doc/00079/19015/16596.pdf
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Fouille de grandes bases de données océaniques: nouveaux défis et solutions. Compte-rendu factuel de l’école d’été OBIDAM14 organisée par l’Ifremer, le CNRS et Telecom Bretagne, 8-9 septembre 2014, Brest ArchiMer
Maze, Guillaume; Mercier, Herle; Fablet, Ronan; Lenca, Philippe; Piolle, Jean-francois.
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Ano: 2014 URL: http://archimer.ifremer.fr/doc/00213/32413/30882.pdf
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Fusion of textural statistics using a similarity measure: application to texture recognition and segmentation ArchiMer
Karoui, I; Fablet, Ronan; Boucher, J; Pieczynski, W; Augustin, Jean-marie.
Features computed as statistics (e.g. histograms) of local filter responses have been reported as the most powerful descriptors for texture classification and segmentation. The selection of the filter banks remains however a crucial issue, as well as determining a relevant combination of these descriptors. To cope with selection and fusion issues, we propose a novel approach relying on the definition of the texture-based similarity measure as a weighted sum of the Kullback-Leibler measures between empirical feature statistics. Within a supervised framework, the weighting factors are estimated according to the maximization of a margin-based criterion. This weighting scheme can also be considered as a filter selection method: texture filter response...
Tipo: Text Palavras-chave: MRF based texture segmentation; Texture recognition; Feature fusion and selection; Non parametric feature statistics.
Ano: 2008 URL: http://archimer.ifremer.fr/doc/2008/publication-4546.pdf
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Importance and future of individual markers for the ecosystem approach to fisheries ArchiMer
Fromentin, Jean-marc; Ernande, Bruno; Fablet, Ronan; De Pontual, Helene.
The use of genetic, biochemical and electronic markers in population biology and ecology has been growing tremendously during the last two decades. The first part of this paper aims at reviewing the main principles and advances of these individual markers through a few key applications on exploited marine fish populations. The second part is more prospective and investigates some possibilities that could arise in the near future through: (i) the development of new markers, (ii) the combination of different markers and (iii) the combination of quantitative approaches-whether classical or new-with individual markers. It is finally stressed how crucial individual markers will be to unravel the biocomplexity of wild fish populations and the key role they...
Tipo: Text Palavras-chave: Genetic marker; Biochemical marker; Electronic tag; Otolith; Isotope; Population structure; Statistical and mechanistic model; Fisheries.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/00000/11163/7522.pdf
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Interpolating orientation fields: An axiomatic approach ArchiMer
Chessel, Anatole; Cao, F; Fablet, Ronan.
We develop an axiomatic approach of vector field interpolation, which is useful as a feature extraction preprocessing step. Two operators will be singled out: the curvature operator, appearing in the total variation minimisation for image restoration and inpainting/disocclusion, and the Absolutely Minimizing Lipschitz Extension (AMLE), already known as a robust and coherent scalar image interpolation technique if we relax slightly the axioms. Numerical results, using a multiresolution scheme, show that they produce fields in accordance with the human perception of edges.
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Ano: 2006 URL: http://archimer.ifremer.fr/doc/00065/17647/15182.pdf
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Interpolation par assimilation variationnelle de séquences multimodales d’images satellitaires de l’océan ArchiMer
Ba, Sileye O.; Corpetti, Thomas; Chapron, Bertrand; Fablet, Ronan.
In this paper we address the problem of missing data interpolation in multi-modal geophysical satellite observation sequences. Main issues relate to the large percentage of missing data, from 20 % to 90 % for daily high-resolution observations; and the requirement for reconstructing fine-scale structures in accordance with the underlying turbulent dynamics. To solve the missing data interpolation problem, a variational data assimilation model is developped. Using synthetic and real ocean surface observations, numerical and qualitative evaluations demonstrate the relevance of two key components of the proposed model: the fusion of multi-modal observations through a geometric front-driven constraint and the proposed variational assimilation setting using an...
Tipo: Text Palavras-chave: Assimilation variationnelle de données; Interpolation de données manquantes; Inpainting.; Data assimilation; Variational method; Missing data interpolation; Geophysical tracers dynamics; Multimodal interpolation.
Ano: 2012 URL: http://archimer.ifremer.fr/doc/00139/24980/23061.pdf
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Methodological developments for improved bottom detection with the ME70 multibeam echosounder ArchiMer
Bourguignon, Sebastien; Berger, Laurent; Scalabrin, Carla; Fablet, Ronan; Mazauric, Valerie.
Multibeam echosounders and sonars are increasingly used in fisheries acoustics for abundance estimation. Because of reduced side-lobe levels in the beam-array pattern, the new Simrad ME70 multibeam echosounder installed on board Ifremer's RV "Thalassa" has been designed to allow improved detection of fish close to the seabed. To achieve this objective, precise and unambiguous detection of the water-bottom interface is required, which raises the issue of bottom detection, especially in the outer beams. The bottom-detection method implemented in the ME70 is based on the amplitude of the reverberated echo. Such an approach is efficient for vertical beams, but less accurate for beams with higher incidence angles, typically 30°–40° for the beam configurations...
Tipo: Text Palavras-chave: Multibeam echosounder; Fisheries; Bottom detection; Acoustics.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/2009/publication-6629.pdf
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Motion recognition using nonparametric image motion models estimated from temporal and multiscale co-occurrence statistics ArchiMer
Fablet, Ronan; Bouthemy, P.
A new approach for motion characterization in image sequences is presented. It relies on the probabilistic modeling of temporal and scale co-occurrence distributions of local motion-related measurements directly computed over image sequences. Temporal multiscale Gibbs models allow us to handle both spatial and temporal aspects of image motion content within a unified statistical framework. Since this modeling mainly involves the scalar product between co-occurrence values and Gibbs potentials, we can formulate and address several fundamental issues: model estimation according to the ML criterion (hence, model training and learning) and motion classification. We have conducted motion recognition experiments over a large set of real image sequences...
Tipo: Text Palavras-chave: Nonparametric motion analysis; Motion recognition; Multiscale analysis; Gibbs models; Co occurrences; ML criterion.
Ano: 2003 URL: http://archimer.ifremer.fr/doc/00000/10714/9323.pdf
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Neural Network Based Kalman Filters for the Spatio-Temporal Interpolation of Satellite-Derived Sea Surface Temperature ArchiMer
Ouala, Said; Fablet, Ronan; Herzet, Cedric; Chapron, Bertrand; Pascual, Ananda; Collard, Fabrice; Gaultier, Lucile.
The forecasting and reconstruction of oceanic dynamics is a crucial challenge. While model driven strategies are still the state-of-the-art approaches in the reconstruction of spatio-temporal dynamics. The ever increasing availability of data collections in oceanography raised the relevance of data-driven approaches as computationally efficient representations of spatio-temporal fields reconstruction. This tools proved to outperform classical state-of-the-art interpolation techniques such as optimal interpolation and DINEOF in the retrievement of fine scale structures while still been computationally efficient comparing to model based data assimilation schemes. However, coupling this data-driven priors to classical filtering schemes limits their potential...
Tipo: Text Palavras-chave: Data assimilation; Dynamical model; Kalman filter; Neural networks; Data-driven models; Interpolation.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00481/59286/61979.pdf
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