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

Authors

DOI:

https://doi.org/10.3989/scimar.04961.15A

Keywords:

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

Abstract


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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References

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. https://doi.org/10.1016/j.asoc.2011.01.020

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. https://www.fisheries.noaa.gov/resource/document/ 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. https://doi.org/10.1139/f86-152

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. https://doi.org/10.1590/S0073-47212012000400005

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. https://doi.org/10.3354/ab00557

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. https://doi.org/10.1139/9780660191089

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. https://doi.org/10.1016/j.jembe.2010.11.011

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. https://doi.org/10.1139/f03-151

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. https://doi.org/10.1016/j.dsr.2017.04.016

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. https://doi.org/10.1139/f81-225

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. https://doi.org/10.1111/j.0022-1112.2004.00558.x

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. https://doi.org/10.1002/iroh.19900750607

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. https://doi.org/10.1139/f68-227

Furlani D., Gales R., Pemberton D. 2007. Otoliths of common Australian temperate fish: a photographic guide, CSIRO Publishing, Collingwood, 208 pp. https://doi.org/10.1071/9780643098459

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. https://doi.org/10.1163/002829684X00290

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. https://doi.org/10.1007/BF02006138

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. https://doi.org/10.1016/0146-664X(82)90034-X

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. https://doi.org/10.1111/j.1095-8649.2007.01465.x

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. https://doi.org/10.1002/jmor.1052140107 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. https://doi.org/10.3989/scimar.2006.70n1147

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. https://doi.org/10.3233/AIC-160715

Marti-Puig P., Danés J., Manjabacas A., et al. 2015. New parameterization method for 3D otolith surface images. Mar. Freshw. Res. 67: 1059-1071. https://doi.org/10.1071/MF15069

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. https://doi.org/10.1016/j.fishres.2005.03.002

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. https://doi.org/10.3354/meps09670

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. https://doi.org/10.1644/12-MAMM-A-281.1

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. https://doi.org/10.1071/MF04162

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. https://doi.org/10.1016/j.fishres.2010.02.005

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. https://doi.org/10.1071/MF04163

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. https://doi.org/10.1111/j.1469-7998.1991.tb04810.x

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. https://doi.org/10.1577/T05-207.1

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. https://doi.org/10.1007/s10641-010-9700-3

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. https://doi.org/10.1002/j.1834-4453.2009.tb00070.x

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. https://doi.org/10.3989/scimar.03982.16C

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. https://doi.org/10.5962/bhl.title.141860

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. https://doi.org/10.1016/j.fishres.2006.06.020

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. https://doi.org/10.3989/scimar.2008.72s17

Tuset V.M., Azzurro E., Lombarte A. 2013. Identification of Lessepsian fish species using the sagittae otolith. Sci. Mar. 76: 289-299. https://doi.org/10.3989/scimar.03420.18E

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. https://doi.org/10.1071/MF15052

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. https://doi.org/10.1080/17451000.2011.578648

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. https://doi.org/10.1007/3-540-45453-5_111

Published

2020-03-30

How to Cite

1.
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 2024Mar.29];84(1):27-3. Available from: https://scientiamarina.revistas.csic.es/index.php/scientiamarina/article/view/1842

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