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2D and 3D image surface descriptors for fish otoliths classification
authors: Ramon Reig i Bolaño (UVIC) Pere Martí i Puig (UVIC) Antoni Lombarte (ICM-CSIC) Vicenç Parisi i Baradad (UPC)
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outline of the talk introduction: fish otoliths, AFORO database
2D contour descriptors new 2D contour descriptors 3D surfaces of otholits: proposal of extension 2nd. order descriptors (UDWT) conclusions
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introduction: morphological description of fish otoliths
drawing graphic representation taxonomy phylogeny paleontology paleoecology trophic relationships archeology digital photographs otolith measurements are used in: taxonomy (species identification) fisheries (stock identification, ageing) functional morphology and ecomorphology
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introduction: AFORO database
assembles image otoliths, morphometrics and shape analysis ICM collection 2456 high resolution images, 776 species and 156 families AFORO: shape analysis of fish otoliths Lombarte, A., Ò. Chic, V. Parisi-Baradad, R. Olivella, J. Piera & E. García-Ladona A web-based environment from shape analysis of fish otoliths. The AFORO database. Scientia Marina 70:
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outline of the talk introduction: fish otoliths, AFORO database
2D contour descriptors new 2D contour descriptors 3D surfaces of otholits: proposal of extension 2nd. order descriptors (UDWT) conclusions
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2D contour descriptors components xy high quality image
binarized image contour lossy equiangular polar code lossless chain code 1st order CSS, curvature scale space wavelet analysis 2nd order
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1st. order: equiangular radial values
robust to affine transformation and origin lossy: non perfect reconstruction from polar to xy coordinates / contour
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outline of the talk introduction: fish otoliths, AFORO database
2D contour descriptors new 2D contour descriptors 3D surfaces of otholits: proposal of extension 2nd. order descriptors (UDWT) conclusions
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new 2D contour descriptors
high quality image components xy binarized image contour reflected contour image 1st order lossless modified chain code lossy direct sampled y code
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binary contour reflexion
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non redundant contour
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1st. order lossless coder: modified chain code
2 7 6 3 chain code : {1, 2, 1, 7, 6, 7, 1, 2, 2, 2, 1, 2, 1, 3, 3} how can avoid jumps 7,0,7,0... in a straight line -22,5º?
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chain {a1a2a3....an} with aiє{0,1,2,3,4,5,6,7}, :
modified chain code : chain {a1a2a3....an} with aiє{0,1,2,3,4,5,6,7}, : modified chain {b1b2b3....bn}, with b0=8 and bi integer minimizing |bi-bi-1| and (bi-ai)mod8 = 0 chain code :{1, 2, 1, 7, 6, 7, 1, 2, 2, 2, 1, 2, 1, 3, 3} {9,10,9,7,6,7,9,10,10,10,9,10,9,11,11} 10 11 9 12 8
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1st. order lossy coder: direct sampled y
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contour reconstruction (lossless vs. lossy)
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outline of the talk introduction: fish otoliths, AFORO database
2D contour descriptors new 2D contour descriptors 3D surfaces of otholits: proposal of extension 2nd. order descriptors (UDWT) conclusions
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3D surfaces of otholits volumetric 3D surface much more details for the classification/description process (i.e. the representation of the acoustic groove) normalized 3D data adquisition and orientation of otolith
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proposal of extension to 3D surfaces
high quality volume surface volume surface reflected on zy plane x z y lossy sampled surface, image on xy
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proposal of extension to 3D surfaces
high quality volume surface volume surface reflected on yx plane z y x lossy sampled surface, image on zx
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outline of the talk introduction: fish otoliths, AFORO database
2D contour descriptors new 2D contour descriptors 3D surfaces of otholits: proposal of extension 2nd. order descriptors (UDWT) conclusions
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2nd. order: UDWT (undecimated wavelet transf.)
vd1 HPa1 va1 vd2 LPa1 HPa2 va2 vd3 LPa2 HPa3 va3 LPa3 ….
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wavelet analysis of lossy sampled y code
approximate (LP) details wav. (HP)
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wavelet analysis of lossless modified chain code
approximate (LP) details wav. (HP)
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outline of the talk introduction: fish otoliths, AFORO database
2D contour descriptors new 2D contour descriptors 3D surfaces of otholits: proposal of extension 2nd. order descriptors (UDWT) conclusions & questions
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conclusions we proposed a new lossy 2D contour coder (sampled y code) and a lossless one (modified chain code): based on reflection extensible to 3D surfaces (lossy sampled y code) can use 2nd. order descriptors drawback: need a normalized adquisition and positioning,
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questions? thank you
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DTW (dynamic time warping), alignment
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DTW (dynamic time warping) algorithm
accumulative differences matrix minimum distance path, backwards
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filterbank
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measure of MCC to find similar descriptors
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introduction: AFORO database
2456 high resolution images, 776 species and 156 families morphometry shape analysis contours: FT (Fourier transform) CSS (curvature space scale) WT (wavelet analysis) authomatic taxonomy identification AFORO: shape analysis of fish otoliths Lombarte, A., Ò. Chic, V. Parisi-Baradad, R. Olivella, J. Piera & E. García-Ladona A web-based environment from shape analysis of fish otoliths. The AFORO database. Scientia Marina 70:
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1st. order: shifted chain code
robust to affine transformation and origin lossless: perfect reconstruction to xy coordinates / contour
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