Skip to main content

2018 | OriginalPaper | Buchkapitel

Multi-modal Image Analysis for Plant Stress Phenotyping

verfasst von : Swati Bhugra, Anupama Anupama, Santanu Chaudhury, Brejesh Lall, Archana Chugh

Erschienen in: Computer Vision, Pattern Recognition, Image Processing, and Graphics

Verlag: Springer Singapore

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

search-config
loading …

Abstract

Drought stress detection involves multi-modal image analysis with high spatio-temporal resolution. Identification of digital traits that characterizes drought stress response (DSR) is challenging due to high volume of image based features. Also, the labelled data that categorizes DSR are either unavailable or subjectively developed, which is a low-throughput and error-prone task. Therefore, we propose a novel framework that provides an automated scoring of DSR based on multi-trait fusion. k-means clustering was used to extract latent drought clusters and the relevant traits were identified using Support Vector Machine-Recursive Feature Extraction (SVM-RFE). Using these traits, SVM based DSR classification model was constructed. The framework has been validated on visible and thermal shoot images of rice plants, yielding 95% accuracy. Various imaging modalities can be integrated with the proposed framework, thus making it scalable as no prior information about the DSR was assumed.

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 "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!

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!

Anhänge
Nur mit Berechtigung zugänglich
Literatur
1.
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
2.
Zurück zum Zitat Ghanem, M.E., Marrou, H., Sinclair, T.R.: Physiological phenotyping of plants for crop improvement. Trends Plant Sci. 20(3), 139–144 (2015)CrossRef Ghanem, M.E., Marrou, H., Sinclair, T.R.: Physiological phenotyping of plants for crop improvement. Trends Plant Sci. 20(3), 139–144 (2015)CrossRef
3.
Zurück zum Zitat Li, L., Zhang, Q., Huang, D.: A review of imaging techniques for plant phenotyping. Sensors 14(11), 20078–20111 (2014)CrossRef Li, L., Zhang, Q., Huang, D.: A review of imaging techniques for plant phenotyping. Sensors 14(11), 20078–20111 (2014)CrossRef
4.
Zurück zum Zitat Singh, A., Ganapathysubramanian, B., Singh, A.K., Sarkar, S.: Machine learning for high-throughput stress phenotyping in plants. Trends Plant Sci. 21(2), 110–124 (2016)CrossRef Singh, A., Ganapathysubramanian, B., Singh, A.K., Sarkar, S.: Machine learning for high-throughput stress phenotyping in plants. Trends Plant Sci. 21(2), 110–124 (2016)CrossRef
5.
Zurück zum Zitat Romer, C., Wahabzada, M., Ballvora, A., Pinto, F., Rossini, M., Panigada, C., Behmann, J., Leon, J., Thurau, C., Bauckhage, C., et al.: Early drought stress detection in cereals: simplex volume maximisation for hyperspectral image analysis. Funct. Plant Biol. 39(11), 878–890 (2012)CrossRef Romer, C., Wahabzada, M., Ballvora, A., Pinto, F., Rossini, M., Panigada, C., Behmann, J., Leon, J., Thurau, C., Bauckhage, C., et al.: Early drought stress detection in cereals: simplex volume maximisation for hyperspectral image analysis. Funct. Plant Biol. 39(11), 878–890 (2012)CrossRef
6.
Zurück zum Zitat Kersting, K., Xu, Z., Wahabzada, M., Bauckhage, C., Thurau, C., Roemer, C., Ballvora, A., Rascher, U., Leon, J., Pluemer, L.: Pre-symptomatic prediction of plant drought stress using Dirichlet aggregation regression on hyperspectral images. In: AAAI (2012) Kersting, K., Xu, Z., Wahabzada, M., Bauckhage, C., Thurau, C., Roemer, C., Ballvora, A., Rascher, U., Leon, J., Pluemer, L.: Pre-symptomatic prediction of plant drought stress using Dirichlet aggregation regression on hyperspectral images. In: AAAI (2012)
7.
Zurück zum Zitat Smith, H.K., Clarkson, G.J., Taylor, G., Thompson, A.J., Clarkson, J., Rajpoot, N.M., et al.: Automatic detection of regions in spinach canopies responding to soil moisture deficit using combined visible and thermal imagery. PLoS ONE 9(6), e97612 (2014)CrossRef Smith, H.K., Clarkson, G.J., Taylor, G., Thompson, A.J., Clarkson, J., Rajpoot, N.M., et al.: Automatic detection of regions in spinach canopies responding to soil moisture deficit using combined visible and thermal imagery. PLoS ONE 9(6), e97612 (2014)CrossRef
8.
Zurück zum Zitat Humplík, J.F., Lazar, D., Husickova, A., Spíchal, L.: Automated phenotyping of plant shoots using imaging methods for analysis of plant stress responses–a review. Plant Methods 11(1), 1 (2015)CrossRef Humplík, J.F., Lazar, D., Husickova, A., Spíchal, L.: Automated phenotyping of plant shoots using imaging methods for analysis of plant stress responses–a review. Plant Methods 11(1), 1 (2015)CrossRef
9.
Zurück zum Zitat Chen, D., Neumann, K., Friedel, S., Kilian, B., Chen, M., Altmann, T., Klukas, C.: Dissecting the phenotypic components of crop plant growth and drought responses based on high-throughput image analysis. Plant Cell 26(12), 4636–4655 (2014)CrossRef Chen, D., Neumann, K., Friedel, S., Kilian, B., Chen, M., Altmann, T., Klukas, C.: Dissecting the phenotypic components of crop plant growth and drought responses based on high-throughput image analysis. Plant Cell 26(12), 4636–4655 (2014)CrossRef
10.
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
11.
Zurück zum Zitat Barrs, H., Weatherley, P.: A re-examination of the relative turgidity technique for estimating water deficits in leaves. Aust. J. Biol. Sci. 15(3), 413–428 (1962)CrossRef Barrs, H., Weatherley, P.: A re-examination of the relative turgidity technique for estimating water deficits in leaves. Aust. J. Biol. Sci. 15(3), 413–428 (1962)CrossRef
12.
Zurück zum Zitat Richardson, A.D., Duigan, S.P., Berlyn, G.P.: An evaluation of noninvasive methods to estimate foliar chlorophyll content. New Phytol. 153(1), 185–194 (2002)CrossRef Richardson, A.D., Duigan, S.P., Berlyn, G.P.: An evaluation of noninvasive methods to estimate foliar chlorophyll content. New Phytol. 153(1), 185–194 (2002)CrossRef
13.
Zurück zum Zitat Munne-Bosch, S., Alegre, L.: Die and let live: leaf senescence contributes to plant survival under drought stress. Funct. Plant Biol. 31(3), 203–216 (2004)CrossRef Munne-Bosch, S., Alegre, L.: Die and let live: leaf senescence contributes to plant survival under drought stress. Funct. Plant Biol. 31(3), 203–216 (2004)CrossRef
14.
Zurück zum Zitat Pask, A., Pietragalla, J.: Leaf area, green crop area and senescence. In: Pask, A., Pietragalla, J., Mullan, D., Reynolds, M. (eds.) Physiological Breeding II: A Field Guide to Wheat Phenotyping, pp. 58–62 (2012) Pask, A., Pietragalla, J.: Leaf area, green crop area and senescence. In: Pask, A., Pietragalla, J., Mullan, D., Reynolds, M. (eds.) Physiological Breeding II: A Field Guide to Wheat Phenotyping, pp. 58–62 (2012)
15.
Zurück zum Zitat Neilson, E.H., Edwards, A., Blomstedt, C., Berger, B., Moller, B.L., Gleadow, R.: Utilization of a high-throughput shoot imaging system to examine the dynamic phenotypic responses of a C4 cereal crop plant to nitrogen and water deficiency over time. J. Exp. Bot. (2015). https://doi.org/10.1093/jxb/eru526 Neilson, E.H., Edwards, A., Blomstedt, C., Berger, B., Moller, B.L., Gleadow, R.: Utilization of a high-throughput shoot imaging system to examine the dynamic phenotypic responses of a C4 cereal crop plant to nitrogen and water deficiency over time. J. Exp. Bot. (2015). https://​doi.​org/​10.​1093/​jxb/​eru526
16.
Zurück zum Zitat Fahlgren, N., Feldman, M., Gehan, M.A., Wilson, M.S., Shyu, C., Bryant, D.W., Hill, S.T., McEntee, C.J., Warnasooriya, S.N., Kumar, I., et al.: A versatile phenotyping system and analytics platform reveals diverse temporal responses to water availability in Setaria. Mol. Plant 8(10), 1520–1535 (2015)CrossRef Fahlgren, N., Feldman, M., Gehan, M.A., Wilson, M.S., Shyu, C., Bryant, D.W., Hill, S.T., McEntee, C.J., Warnasooriya, S.N., Kumar, I., et al.: A versatile phenotyping system and analytics platform reveals diverse temporal responses to water availability in Setaria. Mol. Plant 8(10), 1520–1535 (2015)CrossRef
17.
Zurück zum Zitat Boykov, O.V.Y., Zabih, R.: Fast approximate energy minimization via graph cuts. IEEE Trans. Pattern Anal. Mach. Intell. 23(11), 1 (2001)CrossRef Boykov, O.V.Y., Zabih, R.: Fast approximate energy minimization via graph cuts. IEEE Trans. Pattern Anal. Mach. Intell. 23(11), 1 (2001)CrossRef
18.
Zurück zum Zitat Klukas, C., Chen, D., Pape, J.-M.: Integrated analysis platform: an open-source information system for high-throughput plant phenotyping. Plant Physiol. 165(2), 506–518 (2014)CrossRef Klukas, C., Chen, D., Pape, J.-M.: Integrated analysis platform: an open-source information system for high-throughput plant phenotyping. Plant Physiol. 165(2), 506–518 (2014)CrossRef
19.
Zurück zum Zitat Breiman, L.: Statistics with a View Toward Applications, vol. 1. Houghton Mifflin Co., Boston (1973)MATH Breiman, L.: Statistics with a View Toward Applications, vol. 1. Houghton Mifflin Co., Boston (1973)MATH
20.
Zurück zum Zitat Barber, C.B., Dobkin, D.P., Huhdanpaa, H.: The quickhull algorithm for convex hulls. ACM Trans. Math. Softw. (TOMS) 22(4), 469–483 (1996)MathSciNetCrossRef Barber, C.B., Dobkin, D.P., Huhdanpaa, H.: The quickhull algorithm for convex hulls. ACM Trans. Math. Softw. (TOMS) 22(4), 469–483 (1996)MathSciNetCrossRef
21.
Zurück zum Zitat Jones, H.G., Serraj, R., Loveys, B.R., Xiong, L., Wheaton, A., Price, A.H.: Thermal infrared imaging of crop canopies for the remote diagnosis and quantification of plant responses to water stress in the field. Funct. Plant Biol. 36(11), 978–989 (2009)CrossRef Jones, H.G., Serraj, R., Loveys, B.R., Xiong, L., Wheaton, A., Price, A.H.: Thermal infrared imaging of crop canopies for the remote diagnosis and quantification of plant responses to water stress in the field. Funct. Plant Biol. 36(11), 978–989 (2009)CrossRef
22.
Zurück zum Zitat Leinonen, I., Jones, H.G.: Combining thermal and visible imagery for estimating canopy temperature and identifying plant stress. J. Exp. Bot. 55(401), 1423–1431 (2004)CrossRef Leinonen, I., Jones, H.G.: Combining thermal and visible imagery for estimating canopy temperature and identifying plant stress. J. Exp. Bot. 55(401), 1423–1431 (2004)CrossRef
23.
Zurück zum Zitat Raghunathan, S., Stredney, D., Schmalbrock, P., Clymer, B.D.: Image registration using rigid registration and maximization of mutual information. In: The 13th Annual Medicine Meets Virtual Reality Conference, Poster Presented at: MMVR13 (2005) Raghunathan, S., Stredney, D., Schmalbrock, P., Clymer, B.D.: Image registration using rigid registration and maximization of mutual information. In: The 13th Annual Medicine Meets Virtual Reality Conference, Poster Presented at: MMVR13 (2005)
24.
Zurück zum Zitat MacQueen, J., et al.: Some methods for classification and analysis of multivariate observations. In: Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability, Oakland, CA, USA, vol. 1, no. 14, pp. 281–297 (1967) MacQueen, J., et al.: Some methods for classification and analysis of multivariate observations. In: Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability, Oakland, CA, USA, vol. 1, no. 14, pp. 281–297 (1967)
25.
Zurück zum Zitat Kaufman, L., Rousseeuw, P.J.: Finding Groups in Data: An Introduction to Cluster Analysis, vol. 344. Wiley, Hoboken (2009)MATH Kaufman, L., Rousseeuw, P.J.: Finding Groups in Data: An Introduction to Cluster Analysis, vol. 344. Wiley, Hoboken (2009)MATH
26.
27.
Zurück zum Zitat Maldonado, S., Weber, R.: A wrapper method for feature selection using support vector machines. Inf. Sci. 179(13), 2208–2217 (2009)CrossRef Maldonado, S., Weber, R.: A wrapper method for feature selection using support vector machines. Inf. Sci. 179(13), 2208–2217 (2009)CrossRef
28.
Zurück zum Zitat Cortes, C., Vapnik, V.: Support-vector networks. Mach. Learn. 20(3), 273–297 (1995)MATH Cortes, C., Vapnik, V.: Support-vector networks. Mach. Learn. 20(3), 273–297 (1995)MATH
29.
Zurück zum Zitat Liu, Y., You, Z., Cao, L.: A novel and quick SVM-based multi-class classifier. Pattern Recognit. 39(11), 2258–2264 (2006)CrossRef Liu, Y., You, Z., Cao, L.: A novel and quick SVM-based multi-class classifier. Pattern Recognit. 39(11), 2258–2264 (2006)CrossRef
30.
Zurück zum Zitat Platt, J.C., Cristianini, N., Shawe-Taylor, J.: Large margin DAGs for multiclass classification. In: NIPS, vol. 12, pp. 547–553 (1999) Platt, J.C., Cristianini, N., Shawe-Taylor, J.: Large margin DAGs for multiclass classification. In: NIPS, vol. 12, pp. 547–553 (1999)
31.
Zurück zum Zitat Blum, A.: Effective use of water (EUW) and not water-use efficiency (WUE) is the target of crop yield improvement under drought stress. Field Crop. Res. 112(2), 119–123 (2009)CrossRef Blum, A.: Effective use of water (EUW) and not water-use efficiency (WUE) is the target of crop yield improvement under drought stress. Field Crop. Res. 112(2), 119–123 (2009)CrossRef
Metadaten
Titel
Multi-modal Image Analysis for Plant Stress Phenotyping
verfasst von
Swati Bhugra
Anupama Anupama
Santanu Chaudhury
Brejesh Lall
Archana Chugh
Copyright-Jahr
2018
Verlag
Springer Singapore
DOI
https://doi.org/10.1007/978-981-13-0020-2_24