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  • Application of otolith mass and shape for discriminating scabbardfishes Aphanopus spp. in the north-eastern Atlantic Ocean

     Tuset Andujar, Victor Manuel; Parisi Baradad, Vicenç; Lombarte Carrera, Antonio
    Journal of fish biology
    Vol. 82, num. 5, p. 1746-1752
    DOI: 10.1111/jfb.12101
    Date of publication: 2013-05
    Journal article

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    The otolith was used to investigate the variability between Aphanopus carbo and Aphanopus intermedius inhabiting the north-eastern Atlantic Ocean. The results indicate a high degree of morphological affinity between species and areas; a noticeable metabolic change in the otolith shape was noted in the specimens of A. carbo, which may be related to migrations of individuals from shallow water (closer to the continental coast) to deeper water (archipelagos of Madeira and the Canary Islands). The results suggest a single population for both species in the north-eastern Atlantic Ocean, although not conclusively.

  • On the Automatic Detection of Otolith Features for Fish Species Identification and their Age Estimation  Open access

     Soria Perez, Jose Antonio
    Department of Electronic Engineering, Universitat Politècnica de Catalunya
    Theses

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    L'eix principal d'aquesta tesi tracta sobre la detecció automàtica d'irregularitats en senyals, tant si s'extreuen de les imatges fotogràfiques com si es capturen de sensors electrònics, així com la seva possible aplicació en la detecció d'estructures morfològiques en otòlits de peixos per identificar espècie, i realitzar una estimació de l'edat en el moment de la seva mort. Des de la vesant més biològica, els otòlits, que son estructures calcàries que es troben en el sistema auditiu de tots els peixos teleostis, constitueixen un dels elements principals en l'estudi i la gestió de l'ecologia marina. En aquest sentit, l'ús combinat de descriptors de Fourier i l'anàlisi de components és el primer pas i la clau per caracteritzar la seva morfologia i identificar espècies marines. No obstant, una de les limitacions principals d'aquest sistema de representació consisteix en la interpretació limitada de les irregularitats que pot desenvolupar, així com l'ús que es realitza dels coeficients en tasques de classificació, els quals, acostumen a seleccionar-se manualment tant pel que respecta a la quantitat com la seva importància. La detecció automàtica d'irregularitats en senyals, així com la seva interpretació, es va tractar per primera vegada sota el marc del 'Best-Basis paradigm'. En aquest sentit, l'algorisme Local Discriminant Bases (LDB) de N. Saito es basa en la Transformada Wavelet Discreta (DWT) per descriure el posicionament de característiques dintre de l'espai temporal-freqüencial, i en una mesura discriminant basada en l'energia per guiar la cerca automàtica de característiques dintre d'aquest domini. Propostes més recents basades en funcions de densitat han tratat de superar les limitacions de les mesures d'energia amb un èxit relatiu. No obstant, encara s'han de desenvolupar noves estratègies que siguin més consistents amb la capacitat real de classificació i ofereixin més generalització al reduir la dimensió de les dades d'entrada. La proposta d'aquest treball es centra en un nou marc per senyals unidimensionals. Una de les conclusions principals que s'extreu és que aquesta generalització passa per establir un marc de mesures acotades on els valors reflecteixen la densitat on cap classe es solapa. Això condiciona bastant la selecció de característiques i el tamany del vector necessari per identificar les classes correctament, que s'han d'establir no nomès en base a valors discriminants globals si no també en informació complementària sobre la disposició de les mostres en el domini. Les noves eines s'han utilitzat en diferents estudis d'espècie de lluç, on s'han obtingut bons resultats d'identificació. No obstant, l'aportació principal consisteix en la interpretació que s'extreu de les característiques seleccionades, i que inclou l'estructura d'irregularitats, la posició temporal-freqüencial, extensió i rellevància, que es ressalta sobre la mateixa imatge o senyal. En quan a la determinació de l'edat, s'ha plantejat una nova estratègia de demodulació de senyals per compensar l'efecte del creixement no lineal en els perfils d'intensitat. Tot i que inicialment aquesta tècnica és capaç d'adaptar-se automàticament al creixement individual de cada peix, els resultats amb el LDB suggereixen estudiar l'efecte de les condicions lumíniques sobre els otòlits amb la finalitat de trobar tècniques més fiables per reduir la variació del contrast. Mentrestant s'ha plantejat una nova teoria per realitzar estimacions d'edat en peixos en base als otòlits. Aquesta teoria suggereix que si la corba de creixment és coneguda, el període regular dels anells en el perfil d'intensitat demodulat està relacionat amb la longitud total del radi d'on s'agafa el perfil original. Per tant, si la periodicitat es pot mesurar, es possible conèixer l'edat exacta del peix sense usar extractors de característiques o classificadors, la qual cosa tindria implicacions importants en l'ús de recursos computacionals i en les tècniques actuals d'estimació de l'edat.

    This thesis deals with the automatic detection of features in signals, either extracted from photographs or captured by means of electronic sensors, and its possible application in the detection of morphological structures in fish otoliths so as to identify species and estimate their age at death. From a more biological perspective, otoliths, which are calcified structures located in the auditory system of all teleostean fish, constitute one of the main elements employed in the study and management of marine ecology. In this sense, the application of Fourier descriptors to otolith images, combined with component analysis, is habitually a first and a key step towards characterizing their morphology and identifying fish species. However, some of the main limitations arise from the poor interpretation that can be obtained with this representation and the use that is made of the coefficients, as generally they are selected manually for classification purposes, both in quantity and representativity. The automatic detection of irregularities in signals, and their interpretation, was first addressed in the so-called Best-Basis paradigm. In this sense, Saito's Local discriminant Bases algorithm (LDB) uses the Discrete Wavelet Packet Transform (DWPT) as the main descriptive tool for positioning the irregularities in the time-frequency space, and an energy-based discriminant measure to guide the automatic search of relevant features in this domain. Current density-based proposals have tried to overcome the limitations of the energy-based functions with relatively little success. However, other measure strategies more consistent with the true classification capability, and which can provide generalization while reducing the dimensionality of features, are yet to be developed. The proposal of this work focuses on a new framework for one-dimensional signals. An important conclusion extracted therein is that such generalization involves a mesure system of bounded values representing the density where no class overlaps. This determines severely the selection of features and the vector size that is needed for proper class identification, which must be implemented not only based on global discriminant values but also on the complementary information regarding the provision of samples in the domain. The new tools have been used in the biological study of different hake species, yielding good classification results. However, a major contribution lies on the further interpretation of features the tool performs, including the structure of irregularities, time-frequency position, extension support and degree of importance, which is highlighted automatically on the same images or signals. As for aging applications, a new demodulation strategy for compensating the nonlinear growth effect on the intensity profile has been developed. Although the method is, in principle, able to adapt automatically to the specific growth of individual specimens, preliminary results with LDB-based techniques suggest to study the effect of lighting conditions on the otoliths in order to design more reliable techniques for reducing image contrast variation. In the meantime, a new theoretic framework for otolith-based fish age estimation has been presented. This theory suggests that if the true fish growth curve is known, the regular periodicity of age structures in the demodulated profile is related to the radial length the original intensity profile is extracted from. Therefore, if this periodicity can be measured, it is possible to infer the exact fish age omitting feature extractors and classifiers. This could have important implications in the use of computational resources anc current aging approaches.

    El eje principal de esta tesis trata sobre la detección automática de singularidades en señales, tanto si se extraen de imágenes fotográ cas como si se capturan de sensores electrónicos, así como su posible aplicación en la detección de estructuras morfológicas en otolitos de peces para identi car especies, y realizar una estimación de la edad en el momento de su muerte. Desde una vertiente más biológica, los otolitos, que son estructuras calcáreas alojadas en el sistema auditivo de todos los peces teleósteos, constituyen uno de los elementos principales en el estudio y la gestión de la ecología marina. En este sentido, el uso combinado de descriptores de Fourier y el análisis de componentes es el primer paso y la clave para caracterizar su morfología e identi car especies marinas. Sin embargo, una de las limitaciones principales de este sistema de representación subyace en la interpretación limitada que se puede obtener de las irregularidades, así como el uso que se hace de los coe cientes en tareas de clasi cación que, por lo general, acostumbra a seleccionarse manualmente tanto por lo que respecta a la cantidad y a su importancia. La detección automática de irregularidades en señales, y su interpretación, se abordó por primera bajo el marco del Best-Basis paradigm. En este sentido, el algoritmo Local Discriminant Bases (LDB) de N. Saito utiliza la Transformada Wavelet Discreta (DWT) para describir el posicionamiento de características en el espacio tiempo-frecuencia, y una medida discriminante basada en la energía para guiar la búsqueda automática de características en dicho dominio. Propuestas recientes basadas en funciones de densidad han tratado de superar las limitaciones que presentaban las medidas de energía con un éxito relativo. No obstante, todavía están por desarrollar nuevas estrategias más consistentes con la capacidad real de clasi cación y que ofrezcan mayor generalización al reducir la dimensión de los datos de entrada. La propuesta de este trabajo se centra en un nuevo marco para señales unidimensionales. Una conclusión principal que se extrae es que dicha generalización pasa por un marco de medidas de valores acotados que re ejen la densidad donde las clases no se solapan. Esto condiciona severamente el proceso de selección de características y el tamaño del vector necesario para identi car las clases correctamente, que se ha de establecer no sólo en base a valores discriminantes globales sino también en la información complementaria sobre la disposición de las muestras en el dominio. Las nuevas herramientas han sido utilizadas en el estudio biológico de diferentes especies de merluza, donde se han conseguido buenos resultados de identi cación. No obstante, la contribución principal subyace en la interpretación que dicha herramienta hace de las características seleccionadas, y que incluye la estructura de las irregularidades, su posición temporal-frecuencial, extensión en el eje y grado de relevancia, el cual, se resalta automáticamente sobre la misma imagen o señal. Por lo que respecta a la determinación de la edad, se ha planteado una nueva estrategia de demodulación para compensar el efecto del crecimiento no lineal en los per les de intensidad. Inicialmente, aunque el método implementa un proceso de optimización capaz de adaptarse al crecimiento individual de cada pez automáticamente, resultados preliminares obtenidos con técnicas basadas en el LDB sugieren estudiar el efecto de las condiciones lumínicas sobre los otolitos con el n de diseñar algoritmos que reduzcan la variación del contraste de la imagen más ablemente. Mientras tanto, se ha planteado una nueva teoría para estimar la edad de los peces en base a otolitos. Esta teoría sugiere que si la curva de crecimiento real del pez se conoce, el período regular de los anillos en el per l demodulado está relacionado con la longitud total del radio donde se extrae el per l original. Por tanto, si dicha periodicidad es medible, es posible determinar la edad exacta sin necesidad de utilizar extractores de características o clasi cadores, lo cual tendría implicaciones importantes en el uso de recursos computacionales y en las técnicas actuales de estimación de la edad.

    L'eix principal d'aquesta tesi tracta sobre la detecció automàtica d'irregularitats en senyals, tant si s'extreuen de les imatges fotogrà ques com si es capturen de sensors electrònics, així com la seva possible aplicació en la detecció d'estructures morfològiques en otòlits de peixos per identi car espècies, i realitzar una estimació de l'edat en el moment de la seva mort. Des de la vesant més biològica, els otòlits, que son estructures calcàries que es troben en el sistema auditiu de tots els peixos teleostis, constitueixen un dels elements principals en l'estudi i la gestió de l'ecologia marina. En aquest sentit, l'ús combinat de descriptors de Fourier i l'anàlisi de components es el primer pas i la clau per caracteritzar la seva morfologia i identi car espècies marines. No obstant, una de les limitacions principals d'aquest sistema de representació consisteix en la interpretació limitada de les irregularitats que pot desenvolupar, així com l'ús que es realitza dels coe cients en tasques de classi cació, els quals, acostumen a ser seleccionats manualment tant pel que respecta a la quantitat com la seva importància. La detecció automàtica d'irregularitats en senyals, així com la seva interpretació, es va tractar per primera vegada sota el marc del Best-Basis paradigm. En aquest sentit, l'algorisme Local Discriminant Bases (LDB) de N. Saito es basa en la Transformada Wavelet Discreta (DWT) per descriure el posicionament de característiques dintre de l'espai temporal-freqüencial, i en una mesura discriminant basada en l'energia per guiar la cerca automàtica de característiques dintre d'aquest domini. Propostes més recents basades en funcions de densitat han tractat de superar les limitacions de les mesures d'energia amb un èxit relatiu. No obstant, encara s'han de desenvolupar noves estratègies que siguin més consistents amb la capacitat real de classi cació i ofereixin més generalització al reduir la dimensió de les dades d'entrada. La proposta d'aquest treball es centra en un nou marc per senyals unidimensionals. Una de las conclusions principals que s'extreu es que aquesta generalització passa per establir un marc de mesures acotades on els valors re ecteixin la densitat on cap classe es solapa. Això condiciona bastant el procés de selecció de característiques i la mida del vector necessari per identi car les classes correctament, que s'han d'establir no només en base a valors discriminants globals si no també en informació complementària sobre la disposició de les mostres en el domini. Les noves eines s'han utilitzat en diferents estudis d'espècies de lluç, on s'han obtingut bons resultats d'identi cació. No obstant, l'aportació principal consisteix en la interpretació que l'eina extreu de les característiques seleccionades, i que inclou l'estructura de les irregularitats, la seva posició temporal-freqüencial, extensió en l'eix i grau de rellevància, el qual, es ressalta automàticament sobre les mateixa imatge o senyal. En quan a l'àmbit de determinació de l'edat, s'ha plantejat una nova estratègia de demodulació de senyals per compensar l'efecte del creixement no lineal en els per ls d'intensitat. Tot i que inicialment aquesta tècnica desenvolupa un procés d'optimització capaç d'adaptar-se automàticament al creixement individual de cada peix, els resultats amb el LDB suggereixen estudiar l'efecte de les condicions lumíniques sobre els otòlits amb la nalitat de dissenyar algorismes que redueixin la variació del contrast de les imatges més ablement. Mentrestant s'ha plantejat una nova teoria per realitzar estimacions d'edat en peixos en base als otòlits. Aquesta teoria suggereix que si la corba de creixement és coneguda, el període regular dels anells en el per l d'intensitat demodulat està relacionat amb la longitud total de radi d'on s'agafa el per l original. Per tant, si la periodicitat es pot mesurar, es possible conèixer l'edat exacta del peix sense usar extractors de característiques o classi cadors, la qual cosa tindria implicacions importants en l'ús de recursos computacionals i en les tècniques actuals d'estimació de l'edat.

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    Operators to calculate the derivative of digital signals  Open access

     Ferrer Arnau, Luis Jorge; Mon Gonzalez, Juan; Parisi Baradad, Vicenç
    IMEKO World Congress
    p. 301-306
    Presentation's date: 2013-07-18
    Presentation of work at congresses

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    This paper presents an FIR operator with a very low computational cost for calculating the first derivative of discrete band-limited signals. The basic idea is to use cubic spline polynomials for interpolating among the samples and estimate the derivative of the discrete signal as a derivative of the polynomial. This method also allows estimating the derivative at the points between samples. The main contribution of this work is to develop a highly efficient FIR operator with only 9 coefficients for implementing the derivative operator algorithm. The resulting filter can be easily implemented in a microcontroller or an FPGA since only 5 additions and 3 fixed-point multiplications are necessary. If the frequency range of the input signal is between 0 and 0.2 times the sampling frequency (taking 5 samples per cycle), the maximum error in calculating the derivative does not exceed 1.03 %.

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    Decimator filter based on B-splines  Open access

     Ferrer Arnau, Luis Jorge; Roset Juan, Francesc Xavier; Mon Gonzalez, Juan; Parisi Baradad, Vicenç
    IMEKO World Congress
    p. 421-425
    Presentation's date: 2013-07-18
    Presentation of work at congresses

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    The cascaded integrator-comb (CIC) filters are widely used as decimators in many applications, such as in delta sigma AD converters to decimate the sampled signal on its output. One problem with these filters is that by increasing its order to improve the signal attenuation in the stop band, worsens the passband response. In this paper we propose a so-called least-squares filters (LSF) based on B-splines to improve that response, compensating for CIC filter drop and flattening the magnitude response of the pass band. We also study the relationship between the CIC filters, otherwise called moving average, and the B-splines expanded by an integer factor. We show that the least-squares filters based on B-splines can be decomposed in CIC filters, with a higher order than the splines used, plus a compensator filter. Another important contribution of this work are the FIR approximations of anti-causal IIR filters needed to implement LSFs.

    The cascaded integrator-comb (CIC) filters are widely used as decimators in many applications, such as in delta sigma AD converters to decimate the sampled signal on its output. One problem with these filters is that by increasing its order to improve the signal attenuation in the stop band, worsens the passband response. In this paper we propose a so-called least-squares filters (LSF) based on B-splines to improve that response, compensating for CIC filter drop and flattening the magnitude response of the pass band. We also study the relationship between the CIC filters, otherwise called moving average, and the B-splines expanded by an integer factor. We show that the least-squares filters based on B-splines can be decomposed in CIC filters, with a higher order than the splines used, plus a compensator filter. Another important contribution of this work are the FIR approximations of anti-causal IIR filters needed to implement LSFs.

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    Efficient cubic spline interpolation implemented with FIR filters  Open access

     Ferrer Arnau, Luis Jorge; Reig Bolano, Ramon; Marti Puig, Pere; Manjabacas, A.; Parisi Baradad, Vicenç
    International Journal of Computer Information Systems and Industrial Management Applications
    Vol. 5, p. 098-105
    Date of publication: 2012-06-26
    Journal article

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    Classical Cubic spline interpolation needs to solve a set of equations of high dimension. In this work we show how to compute the interpolant using a FIR digital filter, with a reduced number of operations per interpolated point and high accuracy. Additionally, the computation can be made on real time as the signal samples are acquired. Following this approach, we show how to obtain easily the derivatives of the interpolant in a similar way, and also signal approximations to reduce the oscillations that appear when using high order splines. These techniques are very well suited to compute continuous representations of image contours on closed shapes and to find its curvature and singularities.

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    Data acquisition system for volcanic seismic  Open access

     Carreras Pons, Normandino; Gomariz Castro, Spartacus; Parisi Baradad, Vicenç; Del Rio Fernandez, Joaquin
    Instrumentation viewpoint
    num. 13, p. 16-17
    Date of publication: 2012-12-01
    Journal article

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    This paper presents a design that is being created for the acquisition of volcanic seismic data. This system is composed by a microcontroller to management the peripherals, a module to acquire the information of seismic sensor and the module of communications that is composed of the RF and the GPS system. The prototype will be a very low power system and it will allow work during a complete year.

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    Efficient implementation with FIR filters of operators based on B-splines to represent and classify signals of one and two dimensions  Open access

     Ferrer Arnau, Luis Jorge; Parisi Baradad, Vicenç
    Barcelona Forum on Ph.D. Research in Communication and Information Technologies
    p. 21-22
    Presentation's date: 2012-10-15
    Presentation of work at congresses

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  • AFORO 3D

     Parisi Baradad, Vicenç; Lombarte Carrera, Antonio; Soria Perez, Jose Antonio; Ferrer Arnau, Luis Jorge
    Competitive project

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  • Feature selection for analyzing and retrieving fish otoliths using Elliptic Fourier Descriptors of shapes

     Reig Bolano, Ramon; Marti Puig, Pere; Gallego, Esteve; Masferrer, Gerard; Lombarte Carrera, Antonio; Ferrer Arnau, Luis Jorge; Parisi Baradad, Vicenç
    International Conference on Next Generation Web Services Practices
    p. 290-295
    DOI: 10.1109/NWeSP.2011.6088193
    Presentation's date: 2011-10
    Presentation of work at congresses

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    This paper analyzes the characteristics of an experimental otolith retrieval system based on image contours described with Elliptical Fourier Descriptors (EFD). Otoliths are found in the inner ear of fish. Their shape can be analyzed to determine sex, age, populations and species, and thus they can provide necessary and relevant information for ecological studies. The system we propose was tested by identifying three different species, Engraulis encrasicolus from the family Engraulidae, Pomadasys incisus from the family Haemulidae, and two populations of the species Merluccius merluccius (from Catalonia and Galicia) from the family Merlucciidae. We focus on the search engine, experimenting with two cases and analyzing the feature selection obtained with the EFD coefficients.

  • Best-basis development towards the automatical detection of otolith irregularities in fishes

     Soria Perez, Jose Antonio; Parisi Baradad, Vicenç
    International Conference on Next Generation Web Services Practices
    p. 332-337
    DOI: 10.1109/NWeSP.2011.6088200
    Presentation's date: 2011-10
    Presentation of work at congresses

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    The application of feature extraction methodologies and the detection of patterns in sagitae otoliths, which are calcified structures in the inner ear of teleostean fishes, has lead to great knowledge of marine biology during the last decades in order to manage and control its sustainability. A main limitation of the use of statistical analysis and Fourier methods rely on their incapacity to locate irregularities and explain them from a more structural, or even physical, point of view. This matter has been addressed recently by means of the Best-Basis paradigm which combines robust description methods, such as the Wavelet Transform, and the potential of statistical analysis in order to fully automate the selection process of efficient features. This paper is an attempt to readdress this paradigm towards this goal and contrasts other standard tools used in the field of otolith-based fish recognition. The proposed strategy involves the estimation of class distributions, discriminant measures and the search in the feature space.

  • Efficient representation of contours using splines implemented with FIR filters

     Ferrer Arnau, Luis Jorge; Parisi Baradad, Vicenç; Reig Bolano, Ramon; Marti Puig, Pere; Manjabacas, A.
    International Conference on Next Generation Web Services Practices
    p. 125-128
    DOI: 10.1109/NWeSP.2011.6088164
    Presentation's date: 2011-10
    Presentation of work at congresses

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    The interpolation of contour pixels, with splines, of an order greater than or equal to two, usually causes oscillations that do not fit the original shape. To overcome this we propose using a least squares filter before carrying out the interpolation. This results in a good compromise between the smoothness of the curve and the best fit to the original contour. Representing the contour with a continuous model instead of a discrete model has many advantages for carrying out calculations, as for example the contour curvature, which involves first and second order derivatives, as well as operations that are not well defined in the discrete world. We also present a new way of calculating FIR approximations to filters based on B-splines. The great advantage of this approximation in the case of least squares filter is that it does not need downsampling. This property makes it invariant to translations, and this is very important in classification tasks.

  • Surface parameterization for smooth 3D shapes

     Marti Puig, Pere; Reig Bolano, Ramon; Manjabacas, A.; Ferrer Arnau, Luis Jorge; Parisi Baradad, Vicenç; Lombarte Carrera, Antonio
    International Conference on Next Generation Web Services Practices
    p. 244-249
    DOI: 10.1109/NWeSP.2011.6088185
    Presentation's date: 2011
    Presentation of work at congresses

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    In this work we present a new method for compacting data from 3D shapes by extracting a 3D characteristic curve that we call a 3D signature. The 3D signature obtained preserves almost all the morphological shape information but drastically reduces the number of points required for representing the shape. Furthermore, based on the 3D signature, we present a 2D signature that draws a closed contour in a plane and that can be further compacted using elliptic Fourier descriptors. The method was developed to work with a 3D otolith database that is currently under construction.

  • A new otolith image contour descriptor based on partial reflection

     Reig Bolano, Ramon; Marti Puig, Pere; Lombarte Carrera, Antonio; Soria Perez, Jose Antonio; Parisi Baradad, Vicenç
    Environmental biology of fishes
    Vol. 89, num. 3-4, p. 579-590
    DOI: 10.1007/s10641-010-9700-3
    Date of publication: 2010-12
    Journal article

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  • Otoliths identifiers using image contours EFD

     Reig Bolano, Ramon; Marti Puig, Pere; Rodríguez González, Sara; Bajo Pérez, Javier; Parisi Baradad, Vicenç; Lombarte Carrera, Antonio
    Advances in intelligent and soft computing
    Vol. 79, p. 9-16
    DOI: DOI 10.1007/978-3-642-14883-5
    Date of publication: 2010-09
    Journal article

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    In this paper we analyze the characteristics of an experimental otolith identification system based on image contours described with Elliptical Fourier Descriptors (EFD). Otoliths are found in the inner ear of fishes. They are formed by calcium carbonate crystals and organic materials of proteic origin. Fish otolith shape analysis can be used for sex, age, population and species identification studies, and can provide necessary and relevant information for ecological studies. The system we propose has been tested for the identification of three different species, Engraulis encrasicholus, Pomadasys incisus belonging to the different families (Engroulidae and Haemolidae), and two populations of the species Merluccius merluccius (from CAT and GAL) from the family Merlucciidae. The identification of species from different families could be carried out quite easily with some simple class identifiers -i.e based on Support Vector Machine (SVM) with linear Kernel-; however, to identify these two populations that are characterized by a high similarity in their global form; a more accurate, and detailed shape representation of the otoliths are required, and at the same time the Otolith identifiers have to deal with a bigger number of descriptors. That is the principal reason that makes a challenging task both the design and the training of an otolith identification system, with a good performance on both cases.

  • Automated taxon identification of teleost fishes using an otolith online database-AFORO

     Parisi Baradad, Vicenç; Manjabacas, A.; Lombarte Carrera, Antonio; Olivella, R.; Chic, Oscar; Piera, Jaume; Garcia Ladona, E.
    Fisheries research
    Vol. 105, num. 1, p. 13-20
    DOI: 10.1016/j.fishres.2010.02.005
    Date of publication: 2010-06
    Journal article

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    Automated Taxon Identification (ATI) systems that use a database to identify species or anatomical structures of species from different taxonomical groups have recently been developed. However, few of these works have been applied to marine organisms. In this paper we develop an ATI system for identifying Actynopterigian species from their otolith contour; this is important information for the palaeontological, ictiological and ecological sciences, especially in food web studies. The AFORO website comprises the first web-based automated species identification system based exclusively on otolith shape outline. Species are identified iteratively based on a multiscale representation of the otolith contour. The ATI system is very easy to use as it only requires uploading a suitably oriented otolith image on a black background. Two tests were carried out with a database of 1480 images of left sacullar otoliths (sagittae) from 420 species. The first test analysed 50 different otoliths, 10 per species, from 5 different species. The second test identified 50 otoliths, each from a different species. The two tests obtained similar results (percentage of correct identifications): 72% of specimens were correctly identified at species level, and the percentage increased to 90% at genus level and reached 94% at family level. The best results are obtained for species which have an otolith contour with a very specific morphology, such as the mackerel Scomber colias, and the less efficient results for species with common shaped otoliths with unclear specific characteristics, such as the Mediterranean horse-mackerel Trachurus mediterraneus, or species with large morphological variability between individuals, such as Lophius budegassa or Synodus saurus.

  • Access to the full text
    Density Local Discriminant Bases for the analysis of otolith morphology in fish identification applications  Open access

     Soria Perez, Jose Antonio; Parisi Baradad, Vicenç; Lombarte Carrera, Antonio
    Barcelona Forum on Ph.D. Research in Communications, Electronics and Signal Processing
    p. 23-24
    Presentation's date: 2010-10-21
    Presentation of work at congresses

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  • Radix-R FFT and IFFT factorizations for parallel implementation

     Marti Puig, Pere; Reig Bolano, Ramon; Parisi Baradad, Vicenç
    Advances in soft computing
    Vol. 50, p. 152-160
    DOI: 10.1007/978-3-540-85863-8_19
    Date of publication: 2009
    Journal article

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    Two radix-R regular interconnection pattern families of factorizations for both the FFT and the IFFT -also known as parallel or Pease factorizations- are reformulated and presented. Number R is any power of 2 and N, the size of the transform, any power of R. The first radix-2 parallel FFT algorithm -one of the two known radix-2 topologies- was proposed by Pease. Other authors extended the Pease parallel algorithm to different radix and other particular solutions were also reported. The presented families of factorizations for both the FFT and the IFFT are derived from the well-known Cooley-Tukey factorizations, first, for the radix-2 case, and then, for the general radix-R case. Here we present the complete set of parallel algorithms, that is, algorithms with equal interconnection pattern stage-to-stage topology. In this paper the parallel factorizations are derived by using a unified notation based on the use of the Kronecker product and the even-odd permutation matrix to form the rest of permutation matrices. The radix-R generalization is done in a very simple way. It is shown that, both FFT and IFFT share interconnection pattern solutions. This view tries to contribute to the knowledge of fast parallel algorithms for the case of FFT and IFFT but it can be easily applied to other discrete transforms.

  • A contour based approach for bilateral mammogram registration using discrete wavelet analysis

     Reig Bolano, Ramon; Parisi Baradad, Vicenç; Marti Puig, Pere
    Advances in soft computing
    Vol. 50, p. 347-356
    DOI: 10.1007/978-3-540-85863-8_41
    Date of publication: 2009
    Journal article

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    Registration of mammograms is an essential step to increase the effectiveness of all screening programs planned to early detect breast cancer in asymptomatic women. New techniques based on data fusion of different spatial views, temporal analysis or sequences follow up, and multimodal data analysis, require accurate data registration: forcing spatial alignment of images taken from different views, at different times or from different natures. In this work we will focus on a new technique for automatic bilateral mammograms registration. However the same registration technique is also useful for temporal analysis of the same patient. Bilateral mammogram registration is a challenging task; the mammographic appearance of breast tissue may vary considerably, because of differences in breast compression and positioning, differences in imaging techniques, and changes in the breast itself; moreover, there are no clear landmarks in a mammogram, except for the nipple when it is visible. In our approach we detect the skin-line contour as a first step, we describe the contour as a chain-code, and we make a wavelet based correlation analysis, finally we get the matching of the contours. At the end we apply a global affine transformation.

  • Coding of biosignals using the discrete wavelet decomposition

     Reig Bolano, Ramon; Marti Puig, Pere; Solé-Casals, Jordi; Zaiats, Vladimir; Parisi Baradad, Vicenç
    International conference on non-linear speech processing
    p. 144-151
    DOI: 10.1007/978-3-642-11509-7_19
    Presentation's date: 2009-06
    Presentation of work at congresses

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    Wavelet derived codification techniques are widespread used in image codifiers. The wavelet based compression methods are adequate for representing transients. In this paper we explore the use of the discrete wavelet transform analysis of biological signals in order to improve the data compression capability of data coders. The wavelet analysis provides a subband decomposition of any signal, and this enables a lossless or a lossy implementation with the same architecture. The signals could range from speech to sounds or music, but the approach is more orientated to other biosignals like medical signals EEG, ECG or discrete series. Experimental results based on wavelet coefficients quantification, show a lossless compression of 2:1 in all kind of signals, with a fidelity, measured using PSNR, from 79dB to 100dB, and lossy results preserving most of the signal waveform, with a compression ratio from 3:1 to 5:1, with a fidelity from 25dB to 35 dB.

  • Six years of the interactive AFORO (otolith shape analysis) database website (2003/2009)

     Lombarte Carrera, Antonio; Chic, Oscar; Manjabacas, A.; Olivella, Ramon; Parisi Baradad, Vicenç; Piera, Jaume; Garcia Ladona, E.
    International symposium on fish otolith research and application
    Presentation of work at congresses

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  • 2D and 3D image surface descriptors for fish otoliths classification

     Reig Bolano, Ramon; Marti Puig, Pere; Lombarte Carrera, Antonio; Parisi Baradad, Vicenç
    Workshop in signal processing for marine and seismic data
    Presentation's date: 2009-04-27
    Presentation of work at congresses

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  • Data compression of natural signals based on discrete wavelet transform analysis

     Reig Bolano, Ramon; Marti Puig, Pere; Sole Casals, Jordi; Parisi Baradad, Vicenç
    International conference on non-linear speech processing
    Presentation's date: 2009-06
    Presentation of work at congresses

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    In this paper we explore the use of the discrete wavelet transform analysis of an arbitrary signal in order to improve the data compression capability of data coders. Wavelet analysis is widespread used in image codifiers, for example in JPEG2000. The wavelet compression methods are adequate for representing transients, such as percussion sounds in audio, or high-frequency components in two-dimensional images, for example an image of stars on a night sky. The wavelet analysis provides a subband decomposition of any arbitrary signal, and this enables a lossless or a lossy implementation with the same architecture. The signals could range from speech to sounds or music, but the approach is more orientated to other natural signals like arbitrary discrete series, EEG or ECG. Experimental results based on coefficients quantification, show a loss less compression of 2: I in all kind of signals, and lossy results preserving most of the signal waveform of about 5: I to 3: I.

  • Automatic landmark selection of otolith shape contour using the Wavelet Transform Modulus Maxima

     Torrecilla Ribalta, Elena; Piera, Jaume; Lombarte Carrera, Antonio; Parisi Baradad, Vicenç
    International symposium on fish otolith research and application
    Presentation's date: 2009-09-28
    Presentation of work at congresses

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  • Adecuación de la base de datos de otolitos de la colección ICM al entorno GBIF

     Parisi Baradad, Vicenç; Lombarte Carrera, Antonio
    Competitive project

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  • Local Discriminant Bases Representation and non-linear growth processing for species classification and age estimation of fish based on otolith images

     Soria Perez, Jose Antonio; Parisi Baradad, Vicenç
    Oceans '08 MTS/ IEEE Kobe Techno-Ocean '08
    Presentation of work at congresses

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  • Feature extraction Algorithm

     Parisi Baradad, Vicenç; Soria Perez, Jose Antonio
    Date: 2008-04
    Report

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  • Aplicacions de tècniques de fusió de dades per a l'anàlisi d'imatges de satèl·lit en Oceanografia  Open access

     REIG BOLAÑO, RAMON
    Department of Electronic Engineering, Universitat Politècnica de Catalunya
    Theses

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    Durant dècades s'ha observat i monitoritzat sistemàticament la Terra i el seu entorn des de l'espai o a partir de plataformes aerotransportades. Paral·lelament, s'ha tractat d'extreure el màxim d'informació qualitativa i quantitativa de les observacions realitzades. Les tècniques de fusió de dades donen un "ventall de procediments que ens permeten aprofitar les dades heterogènies obtingudes per diferents mitjans i instruments i integrar-les de manera que el resultat final sigui qualitativament superior". En aquesta tesi s'han desenvolupat noves tècniques que es poden aplicar a l'anàlisi de dades multiespectrals que provenen de sensors remots, adreçades a aplicacions oceanogràfiques. Bàsicament s'han treballat dos aspectes: les tècniques d'enregistrament o alineament d'imatges; i la interpolació de dades esparses i multiescalars, focalitzant els resultats als camps vectorials bidimensionals.En moltes aplicacions que utilitzen imatges derivades de satèl·lits és necessari mesclar o comparar imatges adquirides per diferents sensors, o bé comparar les dades d'un sòl sensor en diferents instants de temps, per exemple en: reconeixement, seguiment i classificació de patrons o en la monitorització mediambiental. Aquestes aplicacions necessiten una etapa prèvia d'enregistrament geomètric, que alinea els píxels d'una imatge, la imatge de treball, amb els píxels corresponents d'una altra imatge, la imatge de referència, de manera que estiguin referides a uns mateixos punts. En aquest treball es proposa una aproximació automàtica a l'enregistrament geomètric d'imatges amb els contorns de les imatges; a partir d'un mètode robust, vàlid per a imatges mutimodals, que a més poden estar afectades de distorsions, rotacions i de, fins i tot, oclusions severes. En síntesi, s'obté una correspondència punt a punt de la imatge de treball amb el mapa de referència, fent servir tècniques de processament multiresolució. El mètode fa servir les mesures de correlació creuada de les transformades wavelet de les seqüències que codifiquen els contorns de la línia de costa. Un cop s'estableix la correspondència punt a punt, es calculen els coeficients de la transformació global i finalment es poden aplicar a la imatge de treball per a enregistrar-la respecte la referència.A la tesi també es prova de resoldre la interpolació d'un camp vectorial espars mostrejat irregularment. Es proposa un algorisme que permet aproximar els valors intermitjos entre les mostres irregulars si es disposa de valors esparsos a escales de menys resolució. El procediment és òptim si tenim un model que caracteritzi l'esquema multiresolució de descomposició i reconstrucció del conjunt de dades. Es basa en la transformada wavelet discreta diàdica i en la seva inversa, realitzades a partir d'uns bancs de filtres d'anàlisi i síntesi. Encara que el problema està mal condicionat i té infinites solucions, la nostra aproximació, que primer treballarem amb senyals d'una dimensió, dóna una estratègia senzilla per a interpolar els valors d'un camp vectorial bidimensional, utilitzant tota la informació disponible a diferents resolucions. Aquest mètode de reconstrucció es pot utilitzar com a extensió de qualsevol interpolació inicial. També pot ser un mètode adequat si es disposa d'un conjunt de mesures esparses de diferents instruments que prenen dades d'una mateixa escena a diferents resolucions, sense cap restricció en les característiques de la distribució de mesures. Inicialment cal un model dels filtres d'anàlisi que generen les dades multiresolució i els filtres de síntesi corresponents, però aquest requeriment es pot relaxar parcialment, i és suficient tenir una aproximació raonable a la part passa baixes dels filtres. Els resultats de la tesi es podrien implementar fàcilment en el flux de processament d'una estació receptora de satèl·lits, i així es contribuiria a la millora d'aplicacions que utilitzessin tècniques de fusió de dades per a monitoritzar paràmetres mediambientals.

    During the last decades a systematic survey of the Earth environment has been set up from many spatial and airborne platforms. At present, there is a continuous effort to extract and combine the maximum of quantitative information from these different data sets, often rather heterogeneous. Data fusion can be defined as "a set of means and tools for the alliance of data originating from different sources with the aims of a greater quality result". In this thesis we have developed new techniques and schemes that can be applied on multispectral data obtained from remote sensors, with particular interest in oceanographic applications. They are based on image and signal processing. We have worked mainly on two topics: image registration techniques or image alignment; and data interpolation of multiscale and sparse data sets, with focus on two dimensional vector fields. In many applications using satellite images, and specifically in those related to oceanographic studies, it is necessary to merge or compare multiple images of the same scene acquired from different captors or from one captor but at different times. Typical applications include pattern classification, recognition and tracking, multisensor data fusion and environmental monitoring. Image registration is the process of aligning the remotely sensed images to the same ground truth and transforming them into a known geographic projection (map coordinates). This step is crucial to correctly merge complementary information from multisensor data. The proposed approach to automatic image registration is a robust method, valid for multimodal images affected by distortions, rotations and, to a reasonably extend, with severe data occlusion. We derived a point to point matching of one image to a georeferenced map applying multiresolution signal processing techniques. The method is based on the contours of images: it uses a maximum cross correlation measure on the biorthogonal undecimated discrete wavelet transforms of the codified coastline contours sequences. Once this point to point correspondence is established, the coefficients of a global transform could be calculated and finally applied on the working image to register it to the georeferenced map. The second topic of this thesis focus on the interpolation of sparse irregularly-sampled vector fields when these sparse data belong to different resolutions. It is proposed a new algorithm to iteratively approximate the intermediate values between irregularly sampled data when a set of sparse values at coarser scales is known. The procedure is optimal if there is a characterized model for the multiresolution decomposition / reconstruction scheme of the dataset. The scheme is based on a fast dyadic wavelet transform and on its inversion using a filter bank analysis/synthesis implementation for the wavelet transform model. Although the problem is ill-posed, and there are infinite solutions, our approach, firstly worked for one dimension signals, gives an easy strategy to interpolate the values of a vector field using all the information available at different scales. This reconstruction method could be used as an extension on any initial interpolation. It can also be suitable in cases where there are sparse measures from different instruments that are sensing the same scene simultaneously at several resolutions, without any restriction to the characteristics of the data distribution. Initially a filter model for the generation of multiresolution data and their synthesis counterpart is the main requisite but; this assumption can be partially relaxed with the only requirement of a reasonable approximation to the low pass counterpart. The thesis results can be easily implemented on the process stream of any satellite receiving station and therefore constitute a first contribution to potential applications on data fusion of environmental monitoring.

  • A recursive approach to multiscalar data interpolation of sparsely sampled sea surface measurements at different spatial resolutions

     Reig Bolano, Ramon; Garcia Ladona, E.; Parisi Baradad, Vicenç; Marti Puig, Pere
    OCEANS MTS/IEEE
    p. 1-7
    DOI: 10.1109/OCEANSKOBE.2008.4530949
    Presentation's date: 2008-04-11
    Presentation of work at congresses

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    In many oceanographic studies there is a need to reconstruct a signal from a set of sparse measurements. We propose an algorithm to iteratively approximate the intermediate values between irregularly sampled data, when a set of sparse values at coarser scales is known. This is possible when there is an approximation to a model for the multiresolution decomposition/reconstruction scheme of the dataset. Although the problem is ill-posed, this approach gives an easy scheme to interpolate the values of a signal using all the information available at different resolutions. This reconstruction method could be used as an extension of any interpolation method to optimize the multiresolution sparse data fusion. A simplified one-dimensional case illustrates the explanation; it is an algorithm based on a recursive scheme of a fast dyadic wavelet transform and its inversion, using a filter bank analysis/synthesis implementation for the wavelet transforms model. This can be a basis method suitable for applied cases where there are sparse measures from different instruments that are sensing the same scene simultaneously with several resolutions. Extensions of the method to sparse multiresolution dataset with higher dimensions (images or vector fields) also offer some promising preliminary results.

  • Satellite image georegistration from coast-line codification  Open access

     Reig Bolano, Ramon; Parisi Baradad, Vicenç; Garcia Ladona, E.; Marti Puig, Pere
    Instrumentation viewpoint
    Vol. 2007, num. 6, p. 83-84
    Date of publication: 2007
    Journal article

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    This paper presents a contour-based approach for automatic image registration in satellite oceanography. Accurate image georegistration is an essential step to increase the eff ectiveness of all the image processing methods that aggregate information from diff erent sources, i.e. applying data fusion techniques. In our approach the images description is based on main contours extracted from coast-line. Each contour is codifi ed by a modifi ed chain-code, and the result is a discrete value sequence. The classical registration techniques were area-based, and the registration was done in a 2D domain (spatial and/or transformed); this approach is feature-based, and the registration is done in a 1D domain (discrete sequences). This new technique improves the registration results. It allows the registration of multimodal images, and the registration when there are occlusions and gaps in the images (i.e. due to clouds), or the registration on images with moderate perspective changes. Finally, it has to be pointed out that the proposed contour-matching technique assumes that a reference image, containing the coastlines of the input image geographical area, is available.

  • A model-based expansion on interpolation for multiresolution sparse data  Open access

     Reig Bolano, Ramon; Parisi Baradad, Vicenç; Garcia Ladona, E.; Marti Puig, Pere
    Instrumentation viewpoint
    Vol. 2007, num. 6, p. 82-83
    Date of publication: 2007
    Journal article

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    This paper addresses the interpolation of sparse irregular data when these sparse data belong to diff erent scales. We propose an algorithm to iteratively approximate the intermediate values between irregularly sampled data, when a set of sparse values at coarser scales is known. This is possible if there is a characterized model for the multiresolution decomposition / reconstruction scheme of the dataset. Although the problem is ill-posed, and there are infi nite solutions, this approach gives an easy scheme to interpolate the values of a signal using all the information available at diff erent scales. This reconstruction method could be used as an extension on any interpolation. A simplifi ed one-dimensional case illustrates the explanation; the scheme is based on a fast dyadic wavelet transform and its inversion, using a fi lter bank analysis/synthesis implementation for the wavelet transforms model. This can be a basis method suitable for applied cases where there are sparse measures from diff erent instruments that are sensing the same scene simultaneously with several resolutions. Extensions of the method to sparse multiresolution data with higher dimensions (images or vector fi elds) also off er some promising preliminary results.

  • Automated FISh Ageing

     Fablet, Ronan; Parisi Baradad, Vicenç; Soria Perez, Jose Antonio
    Competitive project

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  • Local discriminant analysis in automating fish identification and age estimation

     Lombarte, Antonio; Soria Perez, Jose Antonio; Parisi Baradad, Vicenç
    XII Europen Congress of Ichthyology
    p. 225-226
    Presentation of work at congresses

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  • Georeferenciación de imágenes oceanográficas mediante descriptores de contornos

     Reig Bolano, Ramon; Parisi Baradad, Vicenç; Garcia Ladona, E.; Marti Puig, Pere
    Simposium Nacional de la Unión Científica Internacional de Radio
    Presentation of work at congresses

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  • Alineamiento de mamografías mediante descriptores de contornos

     Reig Bolano, Ramon; Juvanteny, Jordi; Parisi Baradad, Vicenç; Marti Puig, Pere
    Simposium Nacional de la Unión Científica Internacional de Radio
    Presentation's date: 2007
    Presentation of work at congresses

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  • A web-based environment for shape analysis of fish otoliths. The AFORO database

     Lombarte Carrera, Antonio; Chic, Oscar; Parisi Baradad, Vicenç; Olivella, Roger; Piera Fernandez, Jaume; Garcia Ladona, E.
    Scientia marina
    Vol. 70, num. 1, p. 147-152
    Date of publication: 2006-01
    Journal article

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  • Bases discriminantes locales para el análisis de señales uridadas aplicadas al estudio de otolitos

     Parisi Baradad, Vicenç; Lombarte, Antonio; Soria Perez, Jose Antonio
    Date: 2006-01
    Report

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  • La pesca en el litoral del Garraf, V trabajo de investigación conjunto IES - EPSEVG

     Del Rio Fernandez, Joaquin; Diaz Boladeras, Marta; Parisi Baradad, Vicenç
    Congreso Universitario de Innovación Educativa en las Enseñanzas Técnicas
    Presentation of work at congresses

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  • Otolith shape feature extraction oriented to automatic classification with open distributed data

     Piera Fernandez, Jaume; Cabestany Moncusi, Joan; Parisi Baradad, Vicenç
    Marine and freshwater research
    Vol. 56, num. 5, p. 805-814
    Date of publication: 2005-09
    Journal article

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  • Otolith shape contour analysis using affine transformation invariant wavelet transforms and curvature scale space representation

     Parisi Baradad, Vicenç; Cabestany Moncusi, Joan; Piera Fernandez, Jaume
    Marine and freshwater research
    Vol. 56, num. 5, p. 795-804
    Date of publication: 2005-09
    Journal article

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  • On-line water monitoring system using a smart array of solid-state chemical sensors

     Bedoya Jimenez, Guillermo; Bermejo Sanchez, Sergio; Cabestany Moncusi, Joan; Parisi Baradad, Vicenç
    2nd International IWA Conference on Automation in Water Quality Monitoring
    p. 289-294
    Presentation of work at congresses

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  • Modeling spatial structures in SST images through Eulian vector fields

     Parisi Baradad, Vicenç; Cabestany Moncusi, Joan; Garcia, E; Font, J
    Proceedings of SPIE, the International Society for Optical Engineering
    Vol. 4172, num. 1, p. 56-64
    Date of publication: 2003-01
    Journal article

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  • Q5RS-2002-01610 IBACS INTEGRATED APPROACH TO THE BIOLOGICAL BASIS OF AGE ESTIMATION IN COMMERCIALLY IMPORTANT FISH SPECIES

     Parisi Baradad, Vicenç; Cabestany Moncusi, Joan; Bermejo Sanchez, Sergio
    Competitive project

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  • Image registration techniques with multiresolution analysis in satellite oceanography

     Bolaño, Ramon Reig; Parisi Baradad, Vicenç; García, Emili Ladona
    DOCUMENTS DE RECERCA. UNIVERSITAT DE VIC
    p. 1-23
    Presentation of work at congresses

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  • Looking at processors for the sewing smart sensor

     Parisi Baradad, Vicenç; Bermejo Sanchez, Sergio; Cabestany Moncusi, Joan
    MIXDES 2002 - 9th INTERNATIONAL CONFERENCE MIXED DESIGN OF INTEGRATED CIRCUITS AND SYSTEMS
    p. 177-180
    Presentation of work at congresses

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  • LOOKING AT PROCESSORS FOR THE SEWING SMART SENSOR

     Parisi Baradad, Vicenç
    MIXDES 2002 - 9th INTERNATIONAL CONFERENCE MIXED DESIGN OF INTEGRATED CIRCUITS AND SYSTEMS
    Presentation's date: 2002-06-20
    Presentation of work at congresses

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