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. 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. 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. 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:

5. 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 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

7. 1st. order: equiangular radial values
robust to affine transformation and origin
lossy: non perfect reconstruction from polar to xy coordinates / contour

8. 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. 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

10. binary contour reflexion

11. non redundant contour

12. 1st. order lossless coder: modified chain code2 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?

13. 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

15. 1st. order lossy coder: direct sampled y

16. contour reconstruction (lossless vs. lossy)

17. 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. 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. 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

20. 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

21. 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. 2nd. order: UDWT (undecimated wavelet transf.)
vd1
HPa1
va1
vd2
LPa1
HPa2
va2
vd3
LPa2
HPa3
va3
LPa3 ….

23. wavelet analysis of lossy sampled y code
approximate (LP) details wav. (HP)

24. wavelet analysis of lossless modified chain code
approximate (LP) details wav. (HP)

25. 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. 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,

27. questions?
thank you

28. DTW (dynamic time warping), alignment

29. DTW (dynamic time warping) algorithm
accumulative differences matrix
minimum distance path, backwards

31. filterbank

32. measure of MCC to find similar descriptors

33. 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:

34. 1st. order: shifted chain code
robust to affine transformation and origin
lossless: perfect reconstruction to xy coordinates / contour