Shape analysis for the automated identification of plants from images of leaves

Taxon

Volumn 58, Issue 3, 2009, Pages 934-954

  Hearn, David J ^a  

^a TOWSON UNIVERSITY   (United States)

Author keywords

Biodiversity informatics; Dichotomous key; Fourier analysis; Leaf shape; Procrustean analysis; Shape representation; Species identification

Indexed keywords

AUTOMATION; BIODIVERSITY; DATABASE; DIGITAL IMAGE; IMAGE RESOLUTION; INFORMATION MANAGEMENT; PLANT COMMUNITY; PROBABILITY; SHAPE ANALYSIS; SOFTWARE; SPECIES DIVERSITY;

EID: 70349664452     PISSN: 00400262     EISSN: None     Source Type: Journal    
DOI: 10.1002/tax.583021     Document Type: Article

References (77)

1. Abbasi, S., Mokhtarian, F. & Kittler, J. 1997. Reliable classification of chrysanthemum leaves through curvature scale space. Pp. 284-295 in: Romeny, B.M., Florack, L.,Koenderink, J.J. & Viergever, M.A. (eds.), Proceedings of the First International Conference on Scale-Space Theory in Computer Vision. Springer, London.
2. Adams, D.C., Rohlf, F.J. & Slice, D.E. 2002. Geometric morphometrics: ten years of progress following the 'Revolution'. Ital. J. Zool. 71: 5-16.
3. Agarwal, G., Belhumeur, P., Feiner, S., Jacobs, D., Kress, W.J., Ramamoorthi, R., Bourg, N.A., Dixit, N., Ling, H., Mahajan, D., Russell, R., Shirdhonkar, S., Sunkavalli, K. & White, S. 2006. First steps toward an electronic field guide for plants. Taxon 55: 597-610.
4. Aleksandrov, A.D., Kolmogorov, A.N. & Lavrent'ev, M.A. (eds.). 1999. Mathematics: Its Contents, Methods, and Meaning. Dover Publications, Inc. Mineola, New York.
5. Alroy, J. 2002. How many named species are valid? Proc. Natl. Acad. Sci. U.S.A. 99: 3706-3711.
6. Atchley, W.R. 1978. On the use of ratios in growth studies. Syst. Zool. 27: 62-67.
7. Atchley, W.R., Gaskins, C.T. & Anderson, D. 1976. Statistical properties of ratios. I. Empirical results. Syst. Zool. 25: 137-148.
8. Bailey, I.W. & Sinnott, E.W. 1916. The climatic distribution of certain types of angiosperm leaves. Amer. J. Bot. 3: 24-39.
9. Belongie, S., Malik, J. & Puzicha, J. 2002. Shape matching and object recognition using shape context. IEEE Transactions on Pattern Analysis and Machine Intelligence 24: 509-522.
10. Bisby, F.A. 2000. The quiet revolution: biodiversity informatics and the Internet. Science 289: 2309-2312.
11. Bookstein, F.L., Strauss, R.E., Humphries, J.M., Chernoff, B., Elder, R.L. & Smith, G.R. 1982. A comment on the uses of Fourier methods in systematics. Syst. Zool. 31: 85-92.
12. Clark, J.Y. & Warwick, K. 1998. Artificial keys for botanical identification using a multiplayer perceptron neural network (MLP). Artificial Intelligence Review 12: 95-115.
13. Dallwitz, M.J. 1974. A flexible computer program for generating identification keys. Syst. Zool. 23: 50-7.
14. Dallwitz, M.J. 1996-. Programs for Interactive Identification Hearn • Leaf shape analysis for automated identification and Information Retrieval. Retrieved 10 October 2008 from http://delta-intkey.com/www/idprogs.htm.
15. Dallwitz, M.J., Paine, T.A. & Zurcher, E.J. 2000. Principles of interactive keys. Retrieved 10 October 2008 from http://delta-intkey.com.
16. Dengsheng, Z. & Guojun, L. 2004. Review of shape representation and description techniques. Pattern Recogniton 37: 1-19.
17. Dickinson, T.A., Parker, W.H. & Strauss, R.E. 1987. Another approach to leaf shape comparisons. Taxon 36: 1-20.
18. Dryden, I.L. & Mardia, K.V. 1998. Statistical Shape Analysis. John Wiley and Sons Ltd., England.
19. Du, J.X., Huang D.S., Wang, X.F. & Gu, X. 2006. Computeraided plant species identification (CAPSI) based on leaf shape matching technique. Trans. Inst. Measurement Control 28: 275-284.
20. Du, J.X., Wang, X.F. & Gu, X. 2005. Shape matching and recognition based on genetic algorithm and application to plant species identification. Lecture Notes Computer Sci. 3644: 282-290.
21. Du, J.X., Wang, X.F. & Zhang, G.J. 2007. Leaf shape based plant species recognition. Appl. Math. Computation 185: 883-893.
22. Duda, R.O., Hart, P.E. & Stork, D.G. 2001. Pattern Classification, 2nd ed. John Wiley & Sons, Inc., New York.
23. Edwards, J.L., Lane, M.A. & Nielsen, E.S. 2000. Interoperability of biodiversity databases: biodiversity information on every desktop. Science 289: 2312-2314.
24. Felsenstein, J. 1985. Phylogenies and the comparative method. Amer. Naturalist 125: 1-15.
25. Fermanian, T.W., Barkworth, M. & Lui, H. 1989. Trained and untrained individual's ability to identify morphological characters of immature grasses. Agron. J. 81: 918-922.
26. Ferson, S., Rohlf, F.J. & Koehn, R.K. 1985. Measuring shape variation of two-dimensional outlines. Syst. Zool. 34: 59-68.
27. Franz, E., Gebhardt, M.R. & Unklesbay, K.B. 1991. Shape description of completely visible and partially occluded leaves for identifying plants in digital images. Trans. Amer. Soc. Agric. Engin. 34: 673-681.
28. Fu, H. & Chi, Z. 2006. Combined thresholding and neural network approach for vein pattern extraction from leaf images. IEE Proceedings Vision, Image & Signal Processing 153: 881-892.
29. Gaston, K. & O'Neill, M. 2004. Automated species identification: Why not? Philos. Trans., Ser. B 359: 655-667.
30. Givnish, T.J. 1978. Ecological aspects of plant morphology: Leaf form in relation to environment. Pp. 83-142 in: Sattler, R. (ed.), Theoretical Plant Morphology. Acta Biotheoretica 27, Supplement: Folia Biotheoretica, No. 7. Leiden University Press, The Hague.
31. Golub, G.H. & van Loan, C.F. 1996. Matrix Computations, 3rd ed. The Johns Hopkins University Press, Baltimore.
32. Goodall, C. 1991. Procrustes methods in the statistical analysis of shape. J. Roy. Statist. Soc., Ser. B 53: 385-339.
33. Govaerts, R. 2001. How many species of seed plants are there? Taxon 50: 1085-1090.
34. Grubb, P.J. 1977. Leaf structure and function. Pp. 317-329 in: Duncan, R. & Weston-Smith, M. (eds.), The Encyclopaedia of Ignorance. Pergamon Press Inc., Oxford, New York.
35. Herbert, P.D.N., Cywinska, A., Ball, S.L. & DeWaard, J.R. 2005. The promise of DNA barcoding for taxonomy. Syst. Biol. 54: 852.
36. Herbert, P.D.N. & Gregory, T.R. 2003. Biological identifications through DNA barcodes. Proc. Roy. Soc. London, Ser. B, Biol. Sci. 270: 313.
37. Kincaid, D.T. & Schneider, R.B. 1983. Quantification of leaf shape with a microcomputer and Fourier transform. Canad. J. Bot. 61: 2333-2342.
38. Kulkarni, S.R. & Posner, S.E. 1995. Rates of convergence of nearest-neighbor estimation under arbitrary sampling. IEEE Transactions on Information Theory 41: 1028-1039.
39. Lee, C.-L. & Chen, S.-Y. 2006. Classification of leaf images. Int. J. Imaging Systems and Technology 16: 15-23.
40. Lele, S. 1991. Some comments on coordinate-free and scaleinvariant methods in morphometrics. Amer. J. Phys. Anthropol. 85: 407-417.
41. Lele, S. 1993. Euclidean distance matrix analysis (EDMA): estimation of mean form and mean form difference. Math. Geol. 25: 573-602.
42. Lesk, A.M. 1994. Computational molecular biology. Pp. 101-165 in: Kent, A. & Williams, J.G., (eds.), Encyclopedia of Computer Science and Technology, vol. 31. Dekker, New York.
43. Lesk, A.M. 1995. Three-dimensional pattern matching in protein structure analysis. Pp. 248-260 in: Goos, G., Hartmanis, J. & van Leeuwen, J. (eds.), Combinatorial Pattern Matching, 6th ed. Springer, Berlin.
44. Lestrel, P. 1997. Fourier Descriptors and their Applications in Biology. Cambridge University Press, Cambridge.
45. Lestrel, P.E. & Roche, A.F. 1986. Cranial base shape variation with age: A longitudinal study of shape using Fourier analysis. Human Biol. 58: 527-540.
46. Ling, H.B. & Jacobs, D.W. 2007. Shape classification using the inner-distance. IEEE Transactions on Pattern Analysis and Machine Intelligence 29: 286-299.
47. Liu, J.S. 2001. Monte Carlo Strategies in Scientific Computing, 2nd ed. Springer, Berlin.
48. Liu, J., Mercer, J.M., Stam, L.F., Gibson, G.C., Zeng, Z.B. & Laurie, C.C. 1996. Genetic analysis of a morphological shape difference in the male genetalia of Drosophila simulans and D. mauritiana. Genetics 142: 1129-1145.
49. Livingston, M. 1996. Landscape Architecture Plant Materials. Retrieved 15 September 2008 from http://ag.arizona.edu/ classes/lar520/.
50. Mahalanobis, P.C. 1936. On the generalized distance in statistics. Proc. Natl. Inst. Sci. India 12: 49-55.
51. McLellan, T. & Endler, J.A. 1998. The relative success of some methods for measuring and describing the shape of complex objects. Syst. Biol. 47: 264-281.
52. Mielke, J. 1993. Native Plants for the Southwestern Landscapes. University of Texas Press, Hong Kong.
53. Mokhtarian, F. & Abbasi, S. 2004. Matching shapes with self-intersections: application to leaf classification. IEEE Transactions on Image Processing 13: 653-661.
54. Nam, Y.Y. & Hwang, E. 2005. A shape-based retrieval scheme for leaf images. Lecture Notes Computer Sci. 3767: 876-887.
55. Neto, J.C., Meyer, G.E., Jones, D.D. & Samal, A.K. 2005. Plant species identification using elliptic Fourier leaf shape analysis. Computers and Electronics in Agriculture 50: 121-134.
56. Osbourne, D.V. 1963. Some aspects of the theory of dichotomous keys. New Phytol. 62: 144-160.
57. Pankhusrt, R.J. (ed.). 1975. Biological Identification with Computers. Academic Press, London.
58. Pankhurst, R.J. 1986. A package of computer programs for handling taxonomic databases. CABIOS 2: 33-39.
59. Paredes, R. & Vidal, E. 2006. Learning weighted metrics to minimize nearest neighbor classification error. IEEE Transactions on Pattern Analysis 28: 1100-1110.
60. Park, J.K., Hwang, E.J. & Nam, Y.Y. 2006. A venation-based leaf image classification scheme. Lecture Notes Computer Sci. 4182: 416-428.
61. Payne, R.W. & Preece, D.A. 1980. Identification keys and diagnostic tables - a review. J. Roy. Statist. Soc., Ser. A 143: 253-292.
62. Payne, R.W. & Thompson, C.J. 1989. A study of criteria for constructing identification keys containing tests with unequal costs. Computational Statist. Quart. 1: 43-52.
63. Premoli, A.C. 1996. Leaf architecture of South American Nothofagus (Nothofagaceae) using traditional and new methods in morphometrics. Bot. J. Linn. Soc. 121: 25-40.
64. Pryer, K.M. & Hearn, D.J. 2009. Evolution of leaf form in marsileaceous ferns: evidence for heterochrony. Evolution 63: 498-513.
65. Ray, T.S. 1992. Landmark eigenshape analysis - homologous contours - leaf shape in Syngonium (Araceae). Amer. J. Bot. 79: 69-76.
66. Rejmánek, M. & Brewer, S.W. 2001. Vegetative identification of tropical woody plants: state of the art and annotated bibliography. Biotropica 33: 214-228.
67. Reynolds, A.P., Dicks, J.L., Roberts, I.N., Wesseliink, J.-J., Iglesia, B., Robert, V., Beokhout, T. & Rayward-Smith, V.J. 2003. Algorithms for identification key generation and optimization with application to yeast identification. Pp. 107-118 in: Cagnoni, S., Cardalda, J.J. Romero, Corne, D., Gottlieb, J., Guillot, A., Hart, E., Johnson, C.G., Marchiori, E., Meyer, J.-A., Middendorf, M. & Raidl, G.R. (eds.), Ap-plications of Evolutionary Computing: EvoBIO, EvoCOP, EvoIASP, EvoMUSART, EvoROB, and EvoSTIM, Essex, UK, April 14-16, 2003, Proceedings. Springer, Berlin.
68. Rohlf, F.J. & Archie, J.W. 1984. A comparison of Fourier methods for the description of wing shape in mosquitoes (Diptera: Culicidae). Syst. Zool. 33: 302-317.
69. Rohlf, F.J. & Slice, D. 1990. Extensions of the Procrustes method for the optimal superimposition of landmarks. Syst. Zool. 39: 40-59.
70. Saitoh, T. & Kaneko, T. 2000. Automatic recognition of wild flowers. Pp. 507-510 in: Proceedings, 15th International Conference on Pattern Recognition, vol. 2. IEEE, Piscataway.
71. Scotland, R.W. & Wortley, A.H. 2003. How many species of seed plants are there? Taxon 52: 101-104.
72. Shannon, C.E. 1948. A mathematical theory of communication. The Bell System Technical Journal 27: 379-423, 623-656.
73. Söderkvist, O. 2001. Computer Vision Classification of Leaves from Swedish Trees. M.Sc. Thesis, Linköping University, Linköping.
74. Wang, Z., Chi, W. & Feng, D. 2003. Shape based leaf image retrieval. IEE Proceedings Vision, Image & Signal Processing 150: 34-43.
75. West, J.G. & Noble, I.R. 1984. Analysis of digitized leaf images of the Dodonaea viscosa complex in Australia. Taxon 33: 595-613.
76. White, R.J., Prentice, H.C. & Verwijst, T. 1988. Automated image acquisition and morphometric description. Canad. J. Bot. 66: 450-459.
77. Woebbecke, D.M., Meyer, G.E., Bargen, K. von, Mortensen, D.A. 1995. Shape features for identifying young weeds using image analysis. Trans. Amer. Soc. Agric. Engin. 38: 271-281.