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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)

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Presentation on theme: "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)"— Presentation transcript:

1 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)

2 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 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

3 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 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

4 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 introduction: AFORO database ICM collection assembles image otoliths, morphometrics and shape analysis 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:

5 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 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

6 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 2D contour descriptors high quality image binarized image contour components xy lossy equiangular polar code lossless chain code CSS, curvature scale space wavelet analysis 1st order 2nd order

7 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 robust to affine transformation and origin lossy: non perfect reconstruction from polar to xy coordinates / contour 1st. order: equiangular radial values

8 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 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

9 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 new 2D contour descriptors high quality image binarized image contour components xy lossy direct sampled y code reflected contour image lossless modified chain code 1st order

10 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 binary contour reflexion

11 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 non redundant contour

12 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 1st. order lossless coder: modified chain code 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?

13 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 modified chain code : chain {a 1 a 2 a 3....a n } with a i є{0,1,2,3,4,5,6,7}, : modified chain{b 1 b 2 b 3....b n }, with b 0 =8 and b i integer minimizing |b i -b i-1 | and (b i -a i )mod8 = 0 chain code :{1, 2, 1, 7, 6, 7, 1, 2, 2, 2, 1, 2, 1, 3, 3} modified chain code : {9,10,9,7,6,7,9,10,10,10,9,10,9,11,11}

14 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32

15 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 1st. order lossy coder: direct sampled y

16 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 contour reconstruction (lossless vs. lossy)

17 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 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

18 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 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

19 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 proposal of extension to 3D surfaces high quality volume surface volume surface reflected on zy plane lossy sampled surface, image on xy x z y

20 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 proposal of extension to 3D surfaces high quality volume surface volume surface reflected on yx plane lossy sampled surface, image on zx z y x

21 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 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

22 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 HPa 1 v vd1 LPa 1 va1 HPa 2 vd2 LPa 2 va2 HPa 3 LPa 3 …. vd3 va3 2nd. order: UDWT (undecimated wavelet transf.)

23 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 wavelet analysis of lossy sampled y code approximate (LP) details wav. (HP)

24 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 wavelet analysis of lossless modified chain code approximate (LP) details wav. (HP)

25 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 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

26 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 conclusions we proposed a new lossy 2D contour coder (sampled y code) and a lossless one (modified chain code): based on reflection based on reflection extensible to 3D surfaces (lossy sampled y code) extensible to 3D surfaces (lossy sampled y code) can use 2nd. order descriptors can use 2nd. order descriptors drawback: need a normalized adquisition and positioning,

27 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 questions? thank you

28 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 DTW (dynamic time warping), alignment

29 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 accumulative differences matrix minimum distance path, backwards DTW (dynamic time warping) algorithm

30 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32

31 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 filterbank

32 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 measure of MCC to find similar descriptors

33 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 introduction: AFORO database 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: 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

34 2D and 3D image surface descriptors for fish otoliths classification – 2nd workshop in signal processing for marine and seismic data, /32 robust to affine transformation and origin lossless: perfect reconstruction to xy coordinates / contour 1st. order: shifted chain code


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