Fourier-based contour descriptors to relax positional standardization of the otolith images in AFORO queries




otoliths, 2D shape descriptors, contour descriptors, rotation invariance, fast Fourier transforms


The otolith digital catalogue AFORO allows unknown otoliths to be classified automatically by using a comparison with its classified records. To do this, the otolith’s contour, which is extracted from an image, is used. In AFORO, otolith images follow a strict positional normalization. Only the left sagitta is considered, and the images must show the internal side of the whole otolith, with the sulcus acusticus visible, the dorsal side (D) placed in the dorsal position and the rostral side (R) placed on the right. The otolith in the incoming image to be classified must also follow the same positional normalization. Variations from the reference position worsen the classification results. In this article, robust contour descriptors are proposed to extend this functionality of AFORO to the images of otoliths that are poorly normalized, contain rotations, are entirely inverted or came from the right rather than the left sagitta. These descriptors are based on the discrete Fourier transform and could extend the classification functionality to incoming images that are taken and sent, for instance, from smartphones in a wide range of working conditions.


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Agarwal M., Venkatraghavan V., Chakraborty C. et al. 2011. A mirror reflection and aspect ratio invariant approach to object recognition using Fourier descriptor. Appl. Soft Computing 11: 3910-3915.

Baldás M.I., Pérez Macri G., Volpedo A.V., et al. 1997. Morfología y morfometría de la sagitta de peces teleósteos del Atlántico Sudoccidental. I: Carangidae, Sciaenidae, Mullidae. Rev. Atlântica 19: 99-112.

Baremore I.E, Bethea D.M. 2005. A guide to otoliths from fishes of the Gulf of Mexico. NOAA Tech. Memorandum NMFS-SEFSC-599. guide-otoliths-fishes-gulf-mexico

Bird J.L., Eppler D.T., Checkley D.M. 1986. Comparison of herring otoliths using Fourier series shape analyses. Can. J. Fish. Aquat. Sci. 43: 1228-1234.

Bustos R.L., Daneri G.A., Harrington A., et al. 2012. The diet of the South American sea lion (Otaria flavescens) at Río Negro, Patagonia, Argentina, during the winter-spring period. Iheringia Sér. Zool. 102: 394-400.

Bustos R.L., Daneri G.A., Volpedo A.V., et al. 2014. Diet of the South American sea lion (Otaria flavescens) during the summer season at Río Negro, Patagonia, Argentina. Aquat. Biol. 20: 235-243.

Campana S.E. 2004. Photographic atlas of fish otoliths of the Northwest Atlantic Ocean. Can. Spec. Publ. Fish. Aquat. Sci. vol. 133, Canadian Sci. Publish., 284 pp.

Capoccioni F., Costa C., Aguzzi J., et al. 2011. Ontogenetic and environmental effects on otolith shape variability in three European eel (Anguilla anguilla, L.) Mediterranean populations. J. Exp. Mar. Biol. Ecol. 397: 1-7.

Cardinale M., Doering-Arjes P., Kastowsky M., et al. 2004. Effects of sex, stock, and environment on the shape of known-age Atlantic cod (Gadus morhua) otoliths. Can. J. Fish. Aquat. Sci. 61: 158-167.

Cartes J.E., Barsanti M., Martínez-Aliaga A., et al. 2017. Recent reconstruction of deep-water macrofaunal communities recorded in Continental Margin sediments in the Balearic Basin. Deep- Sea Res. Part I 125: 52-64.

Casselman J.M., Collins J.J., Crossman E.J., et al. 1981. Lake whitefish (Coregonus clupeaformis) stocks of the Ontario waters of Lake Huron. Can. J. Fish. Aquat. Sci. 38: 1772-1789.

Chaine J., Duvergier J. 1931. Sur les otolithes fossiles de la Catalogne. Publ. Inst. Ciències, InstitucióCatalana d'Història Natural, Memòria 3: 9-38.

Cruz A., Lombarte A. 2004. Otolith size and its relationship with colour patterns and sound production. J. Fish Biol. 65: 1512-1525.

Doering P., Ludwig J. 1990. Shape analysis of otoliths - a tool for indirect ageing of eel, Anguilla anguilla (L.). Int. Rev. Gesamten Hydrobiol. Hydrogr. 75: 737-743.

Fitch J.E., Brownell R.L. 1968. Fish otoliths in cetacean stomachs and their importance in interpreting feeding habits. J. Fish. Res. Board Can. 25: 2561-2574.

Furlani D., Gales R., Pemberton D. 2007. Otoliths of common Australian temperate fish: a photographic guide, CSIRO Publishing, Collingwood, 208 pp.

Gaemers P.A.M. 1984. Taxonomic position of Cichlidae (Pisces, Perciformes) as demonstrated by the morphology of their otoliths. Neth. J. Zool. 34: 566-595.

Hecht T., Appelbaum S. 1982. Morphology and taxonomic significance of the otoliths of some bathypelagic Anguilloidei and Saccopharyngoidei from the Sargasso Sea. Helgol. Meeresunters 35: 301-308.

Koken E. 1884. Ueber Fisch-Otolithen, insbesondere über diejenigen der norddeutschen Oligocän-Ablagerungen. Z. Dtsch. Geol. Ges. Band 36: 500-565.

Kuhl F.P., Giardina C.R. 1982. Elliptic Fourier features of a closed contour. Comp. Graph. Image Proc. 18: 236-258.

Lin C.-H., Chang C.-W. 2012. Otolith atlas of Taiwan fishes. National Museum of Marine Biology and Aquarium, Pingtung.

Lombarte A., Cruz A. 2007. Otolith size trends in marine fish communities from different depth strata. J. Fish Biol. 71: 53-76.

Lombarte A., Fortuño J.M. 1992. Differences in morphological features of the saculus of the inner ear of two hakes (Merluccius capensis and M. paradoxus, Gadiformes) inhabits from different depth of sea. J. Morphol. 214: 97-107. PMid:29865609

Lombarte A., Chic Ò., Parisi-Baradad V., et al. 2006. A web-based environment from shape analysis of fish otoliths. The AFORO database. Sci. Mar. 70: 147-152.

Marti-Puig P., Reig-Bolano R. 2016. A rotation-invariant feature space according to environmental applications needs in a data mining system using fish otoliths. Al Commun. 29: 687-699.

Marti-Puig P., Danés J., Manjabacas A., et al. 2015. New parameterization method for 3D otolith surface images. Mar. Freshw. Res. 67: 1059-1071.

Messieh S., McDougall C., Claytor R. 1989. Separation of Atlantic herring (Clupea harengus) stocks in the Southern Gulf of St. Lawrence using digitised otolith morphometrics and discrimination function analysis. Can. Tech. Rep. Fish. Aquat. Sci. 1647: 1-22.

Monteiro L., Di Beneditto A.P.M., Guilhermo L.H., et al. 2005. Allometric changes and shape differentiation of sagitta otoliths in sciaenid fishes. Fish. Res. 74: 288-299.

Neves V.C., Bried J., Gonzalez-Solis J., et al. 2012. Feeding ecology and movements of the Barolo shearwater Puffinus baroli baroli in the Azores, NE Atlantic. Mar. Ecol. Prog. Ser. 452: 269-285.

Nixon M.S., Aguado A. 2008. Feature Extraction and Image Processing for Computer Vision, Academic Press, Orlando.

Nolf D. 1985. Otolithi piscium. In: Schultze H.P. (eds), Handbook of Paleoichthyology, vol. 10, pp. 1-145. Gustav Fischer Verlag, Stuttgart.

Otalora-Ardila A., Herrera L.G., Flores-Martinez J.J., et al. 2014. Marine and terrestrial food sources in the diet of the fish-eating myotis (Myotis vivesi). J. Mammalogy 94: 1102-1110.

Parisi-Baradad V., Lombarte A., García-Ladona E., et al. 2005. Otolith shape contour analysis using affine transformation invariant wavelet transforms and curvature scale space representation. Mar. Freshw. Res. 56: 795-804.

Parisi-Baradad V., Manjabacas A., Lombarte A., et al. 2010. Automatic taxon identification of teleost fishes in an otolith online database. Fish. Res. 105: 13-20.

Piera J., Parisi-Baradad V., García-Ladona E., et al. 2005. Otolith shape feature extraction oriented to automatic classification with open distributed data. Mar. Freshw. Res. 56: 805-814.

Pierce G.J., Boyle P.R., Diack J.S.W. 1991. Identification of fish otolith and bones in faces and digestive tracts of seals. J. Zool. London 224: 320-328.

Proakis J.G., Manolakis D.G. 1996. Digital Signal Processing. Principles, Algorithms and Applications, Prentice-Hall, New Jersey.

Ramcharitar J., Gannon D.P., Popper A.N. 2006. Bioacoustics of the family Sciaenidae (croakers and drumfishes). Trans. Am. Fish. Soc. 135: 1409-1431.

Reig-Bolaño R., Marti-Puig P., Lombarte A., et al. 2010. A new otolith image contour descriptor based on partial reflection. Environ. Biol. Fish. 89: 579-590.

Rodney H. 2009. The archaeology of the Port Hedland coastal plain and implications for understanding the prehistory of shell mounds and middens in northwestern Australia. Archaeol. Oceania 44: 81-98.

Sadighzadeh Z., Tuset V.M., Dadpour M.R., et al. 2012. Otolith Atlas from the Persian Gulf and the Oman Sea Fishes. Lambert Academic Publications, Saarbrucke, 55 pp.

Sadighzadeh Z., Otero-Ferrer J.L., Lombarte A., et al. 2014. An approach to unraveling the coexistence of snappers (Lutjanidae) using otolith morphology. Sci. Mar. 78: 353-362.

Schmidt W. 1969. The otoliths as a means for differentiation between species of fish of very similar appearance. In: Proceedings-Symposium of Oceanography of Fisheries Research in Tropical Atlantic, (1966 Abidjan, Ivory Coast), pp. 393-396. UNESCO, FAO, OAU.

Smale M.J., Watson G., Hecht T. 1995. Otolith atlas of southern African marine fishes. Ichthyol. Monogr. Ser. n. 1, J.L.B. Smith Inst. Ichthyol., Grahamstown, South Africa, 418 pp.

Tuset V.M., Rosin P.L., Lombarte A. 2006. Sagittae otolith shape used in the identification of fishes of the genus Serranus. Fish. Res. 81: 316-325.

Tuset V.M., Lombarte A., Assis C.A. 2008. Otolith atlas for the western Mediterranean, north and central eastern Atlantic. Sci. Mar. 72 (Suppl. 1): 1-198.

Tuset V.M., Azzurro E., Lombarte A. 2013. Identification of Lessepsian fish species using the sagittae otolith. Sci. Mar. 76: 289-299.

Tuset V.M., Farré M., Otero-Ferrer J.L., et al. 2016. Testing otolith morphology for measuring marine fish biodiversity. Mar. Freshw. Res. 67: 1037-1048.

Veiga P., Xavier J.C., Assis C.A., et al. 2011. Diet of the blue marlin, Makaira nigricans, off the south coast of Portugal. Mar. Biol. Res. 7: 820-825.

Volpedo A.V., Echeverría D.D. 2000. Catálogo y claves de otolitos para la identificación de peces del Mar Argentino 1. Peces de Importáncia Económica. Dunken, Buenos Aires.

Zhang D., Lu G. 2001. A comparison of shape retrieval using Fourier descriptors and short-time Fourier descriptors. In: Shum H.Y., Liao M., Chang S.F. (eds), Advances in Multimedia Information Processing. PCM Lecture Notes in Computer Science, vol 2195. pp. 855-860. Springer, Berlin, Heidelberg.



How to Cite

Marti-Puig P, Manjabacas A, Lombarte A. Fourier-based contour descriptors to relax positional standardization of the otolith images in AFORO queries. Sci. mar. [Internet]. 2020Mar.30 [cited 2024May21];84(1):27-3. Available from:




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