Skip to main content
Erschienen in: Machine Vision and Applications 1-2/2020

01.02.2020 | Original Paper

Rosette plant segmentation with leaf count using orthogonal transform and deep convolutional neural network

verfasst von: J. Praveen Kumar, S. Domnic

Erschienen in: Machine Vision and Applications | Ausgabe 1-2/2020

Einloggen

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config
loading …

Abstract

Plant image analysis plays an important role in agriculture. It is used to record the morphological plant traits regularly and accurately. The plant growth is one of the key traits to be analyzed, which relies on leaf area (i.e., leaf region or plant region) and leaf count. One of the ways to find the leaf count is counting the leaves using segmented plant region. In this paper, a new plant region segmentation scheme is proposed in the orthogonal transform domain based on orthogonal transform coefficients. Initially, an analysis of orthogonal transform coefficients is carried out in terms of the response of orthogonal basis vectors to extract the plant region. After extracting the plant region, the L*a*b and CMYK color spaces are used for noise removal in the segmentation scheme. Finally, the leaves are counted using fine-tuned deep convolutional neural network models. The proposed scheme is experimented on CVPPP benchmark datasets and also tested with the images taken from mobile phone to ensure its reliability and cross-platform applicability. The experiment results on CVPPP benchmark datasets are promising.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

Literatur
1.
Zurück zum Zitat Achanta, R., Shaji, A., Smith, K., Lucchi, A., Fua, P., Süsstrunk, S., et al.: SLIC superpixels compared to state-of-the-art superpixel methods. IEEE Trans. Pattern Anal. Mach. Intell. 34(11), 2274–2282 (2012)CrossRef Achanta, R., Shaji, A., Smith, K., Lucchi, A., Fua, P., Süsstrunk, S., et al.: SLIC superpixels compared to state-of-the-art superpixel methods. IEEE Trans. Pattern Anal. Mach. Intell. 34(11), 2274–2282 (2012)CrossRef
2.
Zurück zum Zitat Adams, R., Bischof, L.: Seeded region growing. IEEE Trans. Pattern Anal. Mach. Intell. 16(6), 641–647 (1994)CrossRef Adams, R., Bischof, L.: Seeded region growing. IEEE Trans. Pattern Anal. Mach. Intell. 16(6), 641–647 (1994)CrossRef
3.
Zurück zum Zitat Aich, S., Stavness, I.: Leaf counting with deep convolutional and deconvolutional networks. In: Proceedings of the 2017 IEEE International Conference on Computer Vision Workshops (ICCVW), pp. 22–29, Venice, Italy (2017) Aich, S., Stavness, I.: Leaf counting with deep convolutional and deconvolutional networks. In: Proceedings of the 2017 IEEE International Conference on Computer Vision Workshops (ICCVW), pp. 22–29, Venice, Italy (2017)
4.
Zurück zum Zitat An, N., Palmer, C.M., Baker, R.L., Markelz, R.J.C., Ta, J., Covington, M.F., Maloof, J.N., Welch, S.M., Weinig, C.: Plant high-throughput phenotyping using photogrammetry and imaging techniques to measure leaf length and rosette area. Comput. Electron. Agric. 127, 376–394 (2016)CrossRef An, N., Palmer, C.M., Baker, R.L., Markelz, R.J.C., Ta, J., Covington, M.F., Maloof, J.N., Welch, S.M., Weinig, C.: Plant high-throughput phenotyping using photogrammetry and imaging techniques to measure leaf length and rosette area. Comput. Electron. Agric. 127, 376–394 (2016)CrossRef
5.
Zurück zum Zitat Arbelaez, P., Maire, M., Fowlkes, C., Malik, J.: Contour detection and hierarchical image segmentation. IEEE Trans. Pattern Anal. Mach. Intell. 33(5), 898–916 (2011)CrossRef Arbelaez, P., Maire, M., Fowlkes, C., Malik, J.: Contour detection and hierarchical image segmentation. IEEE Trans. Pattern Anal. Mach. Intell. 33(5), 898–916 (2011)CrossRef
6.
Zurück zum Zitat Cerutti, G., Tougne, L., Vacavant, A., Coquin, D.: A parametric active polygon for leaf segmentation and shape estimation. In: International Symposium on Visual Computing, pp. 202–213. Springer (2011) Cerutti, G., Tougne, L., Vacavant, A., Coquin, D.: A parametric active polygon for leaf segmentation and shape estimation. In: International Symposium on Visual Computing, pp. 202–213. Springer (2011)
7.
Zurück zum Zitat Chiang, T.-W., Tsai, T., Lin, Y.-C.: Progressive pattern matching approach using discrete cosine transform. In: Proceedings, International Computer Symposium, pp. 726–730, Taipei, Taiwan (2004) Chiang, T.-W., Tsai, T., Lin, Y.-C.: Progressive pattern matching approach using discrete cosine transform. In: Proceedings, International Computer Symposium, pp. 726–730, Taipei, Taiwan (2004)
8.
Zurück zum Zitat De Vylder, J., Ochoa, D., Philips, W., Chaerle, L., Van Der Straeten, D.: Leaf segmentation and tracking using probabilistic parametric active contours. In: International Conference on Computer Vision/Computer Graphics Collaboration Techniques and Applications, pp. 75–85. Springer (2011) De Vylder, J., Ochoa, D., Philips, W., Chaerle, L., Van Der Straeten, D.: Leaf segmentation and tracking using probabilistic parametric active contours. In: International Conference on Computer Vision/Computer Graphics Collaboration Techniques and Applications, pp. 75–85. Springer (2011)
9.
Zurück zum Zitat De Vylder, J., Vandenbussche, F., Hu, Y., Philips, W., Van Der Straeten, D.: Rosette tracker: an open source image analysis tool for automatic quantification of genotype effects. Plant Physiol. 160(3), 1149–1159 (2012)CrossRef De Vylder, J., Vandenbussche, F., Hu, Y., Philips, W., Van Der Straeten, D.: Rosette tracker: an open source image analysis tool for automatic quantification of genotype effects. Plant Physiol. 160(3), 1149–1159 (2012)CrossRef
10.
Zurück zum Zitat Dellen, B., Scharr, H., Torras, C.: Growth signatures of rosette plants from time-lapse video. IEEE/ACM Trans. Comput. Biol. Bioinform. 12(6), 1470–1478 (2015)CrossRef Dellen, B., Scharr, H., Torras, C.: Growth signatures of rosette plants from time-lapse video. IEEE/ACM Trans. Comput. Biol. Bioinform. 12(6), 1470–1478 (2015)CrossRef
11.
Zurück zum Zitat Furbank, R.T., Tester, M.: Phenomics—technologies to relieve the phenotyping bottleneck. Trends Plant Sci. 16(12), 635–644 (2011)CrossRef Furbank, R.T., Tester, M.: Phenomics—technologies to relieve the phenotyping bottleneck. Trends Plant Sci. 16(12), 635–644 (2011)CrossRef
12.
Zurück zum Zitat Giuffrida, M.V., Doerner, P., Tsaftaris, S.A.: Pheno-deep counter: a unified and versatile deep learning architecture for leaf counting. Plant J. 96, 880–890 (2018)CrossRef Giuffrida, M.V., Doerner, P., Tsaftaris, S.A.: Pheno-deep counter: a unified and versatile deep learning architecture for leaf counting. Plant J. 96, 880–890 (2018)CrossRef
13.
Zurück zum Zitat Giuffrida, M.V., Minervini, M., Tsaftaris, S.A.: Learning to count leaves in rosette plants (2016) Giuffrida, M.V., Minervini, M., Tsaftaris, S.A.: Learning to count leaves in rosette plants (2016)
14.
Zurück zum Zitat Grand-Brochier, M., Vacavant, A., Cerutti, G., Kurtz, C., Weber, J., Tougne, L.: Tree leaves extraction in natural images: comparative study of preprocessing tools and segmentation methods. IEEE Trans. Image Process. 24(5), 1549–1560 (2015)MathSciNetCrossRef Grand-Brochier, M., Vacavant, A., Cerutti, G., Kurtz, C., Weber, J., Tougne, L.: Tree leaves extraction in natural images: comparative study of preprocessing tools and segmentation methods. IEEE Trans. Image Process. 24(5), 1549–1560 (2015)MathSciNetCrossRef
15.
Zurück zum Zitat Haris, K., Efstratiadis, S.N., Maglaveras, N., Katsaggelos, A.K.: Hybrid image segmentation using watersheds and fast region merging. IEEE Trans. Image Process. 7(12), 1684–1699 (1998)CrossRef Haris, K., Efstratiadis, S.N., Maglaveras, N., Katsaggelos, A.K.: Hybrid image segmentation using watersheds and fast region merging. IEEE Trans. Image Process. 7(12), 1684–1699 (1998)CrossRef
16.
Zurück zum Zitat Jin, F., Fieguth, P., Winger, L., Jernigan, E.: Adaptive Wiener filtering of noisy images and image sequences. In: Proceedings 2003 International Conference on Image Processing (Cat. No. 03CH37429), vol. 3, pp. III–349. IEEE (2003) Jin, F., Fieguth, P., Winger, L., Jernigan, E.: Adaptive Wiener filtering of noisy images and image sequences. In: Proceedings 2003 International Conference on Image Processing (Cat. No. 03CH37429), vol. 3, pp. III–349. IEEE (2003)
17.
Zurück zum Zitat Kim, G., Xing, E.P., Fei-Fei, L., Kanade, T.: Distributed cosegmentation via submodular optimization on anisotropic diffusion. In: 2011 International Conference on Computer Vision, pp. 169–176. IEEE (2011) Kim, G., Xing, E.P., Fei-Fei, L., Kanade, T.: Distributed cosegmentation via submodular optimization on anisotropic diffusion. In: 2011 International Conference on Computer Vision, pp. 169–176. IEEE (2011)
18.
Zurück zum Zitat Koornneef, M., Hanhart, C., van Loenen-Martinet, P., de Vries, H.B.: The effect of daylength on the transition to flowering in phytochrome-deficient, late-flowering and double mutants of Arabidopsis thaliana. Physiol. Plant. 95(2), 260–266 (1995)CrossRef Koornneef, M., Hanhart, C., van Loenen-Martinet, P., de Vries, H.B.: The effect of daylength on the transition to flowering in phytochrome-deficient, late-flowering and double mutants of Arabidopsis thaliana. Physiol. Plant. 95(2), 260–266 (1995)CrossRef
19.
Zurück zum Zitat Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. In: Advances in Neural Information Processing Systems, pp. 1097–1105 (2012) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. In: Advances in Neural Information Processing Systems, pp. 1097–1105 (2012)
20.
Zurück zum Zitat Kumar, J.P., Domnic, S.: Image based leaf segmentation and counting in rosette plants. Inf. Process. Agric. 6(2), 233–246 (2019) Kumar, J.P., Domnic, S.: Image based leaf segmentation and counting in rosette plants. Inf. Process. Agric. 6(2), 233–246 (2019)
21.
Zurück zum Zitat Lakshmi Priya, G.G., Domnic, S.: Walsh–Hadamard transform kernel-based feature vector for shot boundary detection. IEEE Trans. Image Process. 23(12), 5187–5197 (2014)MathSciNetCrossRef Lakshmi Priya, G.G., Domnic, S.: Walsh–Hadamard transform kernel-based feature vector for shot boundary detection. IEEE Trans. Image Process. 23(12), 5187–5197 (2014)MathSciNetCrossRef
22.
Zurück zum Zitat Lam, E.Y., Goodman, J.W.: A mathematical analysis of the DCT coefficient distributions for images. IEEE Trans. Image Process. 9(10), 1661–1666 (2000)CrossRef Lam, E.Y., Goodman, J.W.: A mathematical analysis of the DCT coefficient distributions for images. IEEE Trans. Image Process. 9(10), 1661–1666 (2000)CrossRef
23.
Zurück zum Zitat Minervini, M., Abdelsamea, M.M., Tsaftaris, S.A.: Image-based plant phenotyping with incremental learning and active contours. Ecol. Inform. 23, 35–48 (2014)CrossRef Minervini, M., Abdelsamea, M.M., Tsaftaris, S.A.: Image-based plant phenotyping with incremental learning and active contours. Ecol. Inform. 23, 35–48 (2014)CrossRef
24.
Zurück zum Zitat Minervini, M., Fischbach, A., Scharr, H., Tsaftaris, S.A.: Finely-grained annotated datasets for image-based plant phenotyping. Pattern Recognit. Lett. 81, 80–89 (2016)CrossRef Minervini, M., Fischbach, A., Scharr, H., Tsaftaris, S.A.: Finely-grained annotated datasets for image-based plant phenotyping. Pattern Recognit. Lett. 81, 80–89 (2016)CrossRef
25.
Zurück zum Zitat Minervini, M., Scharr, H., Tsaftaris, S.A.: Image analysis: the new bottleneck in plant phenotyping [applications corner]. IEEE Signal Process. Mag. 32(4), 126–131 (2015)CrossRef Minervini, M., Scharr, H., Tsaftaris, S.A.: Image analysis: the new bottleneck in plant phenotyping [applications corner]. IEEE Signal Process. Mag. 32(4), 126–131 (2015)CrossRef
26.
Zurück zum Zitat Ning, J., Zhang, L., Zhang, D., Chengke, W.: Interactive image segmentation by maximal similarity based region merging. Pattern Recognit. 43(2), 445–456 (2010)CrossRef Ning, J., Zhang, L., Zhang, D., Chengke, W.: Interactive image segmentation by maximal similarity based region merging. Pattern Recognit. 43(2), 445–456 (2010)CrossRef
27.
Zurück zum Zitat Orlando, F., Napoli, M., Dalla Marta, A., Natali, F., Mancini, M., Zanchi, C., Orlandini, S.: Growth and development responses of tobacco (Nicotiana tabacum L.) to changes in physical and hydrological soil properties due to minimum tillage. Am. J. Plant Sci. 2(3), 334 (2011)CrossRef Orlando, F., Napoli, M., Dalla Marta, A., Natali, F., Mancini, M., Zanchi, C., Orlandini, S.: Growth and development responses of tobacco (Nicotiana tabacum L.) to changes in physical and hydrological soil properties due to minimum tillage. Am. J. Plant Sci. 2(3), 334 (2011)CrossRef
28.
Zurück zum Zitat Pape, J.-M., Klukas, C.: 3-D histogram-based segmentation and leaf detection for rosette plants. In: European Conference on Computer Vision, pp. 61–74. Springer (2014) Pape, J.-M., Klukas, C.: 3-D histogram-based segmentation and leaf detection for rosette plants. In: European Conference on Computer Vision, pp. 61–74. Springer (2014)
29.
Zurück zum Zitat Scharr, H., Minervini, M., French, A.P., Klukas, C., Kramer, D.M., Liu, X., Luengo, I., Pape, J.-M., Polder, G., Vukadinovic, D., et al.: Leaf segmentation in plant phenotyping: a collation study. Mach. Vis. Appl. 27(4), 585–606 (2016)CrossRef Scharr, H., Minervini, M., French, A.P., Klukas, C., Kramer, D.M., Liu, X., Luengo, I., Pape, J.-M., Polder, G., Vukadinovic, D., et al.: Leaf segmentation in plant phenotyping: a collation study. Mach. Vis. Appl. 27(4), 585–606 (2016)CrossRef
30.
Zurück zum Zitat Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:​1409.​1556 (2014)
31.
Zurück zum Zitat Tang, X., Liu, M., Zhao, H., Tao, W.: Leaf extraction from complicated background. In: 2nd International Congress on Image and Signal Processing, 2009, CISP’09, pp. 1–5. IEEE (2009) Tang, X., Liu, M., Zhao, H., Tao, W.: Leaf extraction from complicated background. In: 2nd International Congress on Image and Signal Processing, 2009, CISP’09, pp. 1–5. IEEE (2009)
32.
Zurück zum Zitat Telfer, A., Bollman, K.M., Poethig, R.S.: Phase change and the regulation of trichome distribution in Arabidopsis thaliana. Development 124(3), 645–654 (1997) Telfer, A., Bollman, K.M., Poethig, R.S.: Phase change and the regulation of trichome distribution in Arabidopsis thaliana. Development 124(3), 645–654 (1997)
33.
Zurück zum Zitat Tsai, T., Huang, Y.-P., Chiang, T.-W.: Image retrieval based on dominant texture features. In: IEEE International Symposium on Industrial Electronics, vol. 1, pp. 441–446. IEEE (2006) Tsai, T., Huang, Y.-P., Chiang, T.-W.: Image retrieval based on dominant texture features. In: IEEE International Symposium on Industrial Electronics, vol. 1, pp. 441–446. IEEE (2006)
34.
Zurück zum Zitat Ubbens, J., Cieslak, M., Prusinkiewicz, P., Stavness, I.: The use of plant models in deep learning: an application to leaf counting in rosette plants. Plant Methods 14(1), 6 (2018)CrossRef Ubbens, J., Cieslak, M., Prusinkiewicz, P., Stavness, I.: The use of plant models in deep learning: an application to leaf counting in rosette plants. Plant Methods 14(1), 6 (2018)CrossRef
35.
Zurück zum Zitat Vukadinovic, D., Polder, G.: Watershed and supervised classification based fully automated method for separate leaf segmentation. In: The Netherland Congress on Computer Vision, pp. 1–2 (2015) Vukadinovic, D., Polder, G.: Watershed and supervised classification based fully automated method for separate leaf segmentation. In: The Netherland Congress on Computer Vision, pp. 1–2 (2015)
36.
Zurück zum Zitat Walter, A., Schurr, U.: The modular character of growth in Nicotiana tabacum plants under steady-state nutrition. J. Exp. Bot. 50(336), 1169–1177 (1999)CrossRef Walter, A., Schurr, U.: The modular character of growth in Nicotiana tabacum plants under steady-state nutrition. J. Exp. Bot. 50(336), 1169–1177 (1999)CrossRef
37.
Zurück zum Zitat Bo, W., Nevatia, R.: Detection and segmentation of multiple, partially occluded objects by grouping, merging, assigning part detection responses. Int. J. Comput. Vis. 82(2), 185–204 (2009)CrossRef Bo, W., Nevatia, R.: Detection and segmentation of multiple, partially occluded objects by grouping, merging, assigning part detection responses. Int. J. Comput. Vis. 82(2), 185–204 (2009)CrossRef
38.
Zurück zum Zitat Yin, X., Liu, X., Chen, J., Kramer, D.M.: Multi-leaf tracking from fluorescence plant videos. In: 2014 IEEE International Conference on Image Processing (ICIP), pp. 408–412. IEEE (2014) Yin, X., Liu, X., Chen, J., Kramer, D.M.: Multi-leaf tracking from fluorescence plant videos. In: 2014 IEEE International Conference on Image Processing (ICIP), pp. 408–412. IEEE (2014)
39.
Zurück zum Zitat Zhang, L., Gu, Z., Li, H.: SDSP: a novel saliency detection method by combining simple priors. In: 2013 20th IEEE International Conference on Image Processing (ICIP), pp. 171–175. IEEE (2013) Zhang, L., Gu, Z., Li, H.: SDSP: a novel saliency detection method by combining simple priors. In: 2013 20th IEEE International Conference on Image Processing (ICIP), pp. 171–175. IEEE (2013)
Metadaten
Titel
Rosette plant segmentation with leaf count using orthogonal transform and deep convolutional neural network
verfasst von
J. Praveen Kumar
S. Domnic
Publikationsdatum
01.02.2020
Verlag
Springer Berlin Heidelberg
Erschienen in
Machine Vision and Applications / Ausgabe 1-2/2020
Print ISSN: 0932-8092
Elektronische ISSN: 1432-1769
DOI
https://doi.org/10.1007/s00138-019-01056-2

Weitere Artikel der Ausgabe 1-2/2020

Machine Vision and Applications 1-2/2020 Zur Ausgabe