Prusinkiewicz P, Lindenmayer A. The Algorithmic Beauty of Plants. Berlin: Springer; 2004.
Google Scholar
Godin C. Representing and encoding plant architecture: a review. Ann Forest Sci. 2000; 57(5):413–38.
Article
Google Scholar
Leitner D, Klepsch S, Bodner G, Schnepf A. A dynamic root system growth model based on L-systems. Plant and Soil. 2010; 332(1-2):177–92.
Article
CAS
Google Scholar
Benoit L, Rousseau D, Belin É, Demilly D, Chapeau-Blondeau F. Simulation of image acquisition in machine vision dedicated to seedling elongation to validate image processing root segmentation algorithms. Comput Electron Agric. 2014; 104:84–92.
Article
Google Scholar
Dufour-Kowalski S, Pradal C, Donès N, Barbier De Reuille P, Boudon F, Chopard J, et al. OpenAlea: An open-software plateform for the integration of heterogenous FSPM components. In: 5th International Workshop on Functional-Structural Plant Models, FSPM07, November, 2007. Napier, New Zealand: The Horticulture and Food Research Institute of New Zealand Ltd.: 2007. p. 1–2.
Google Scholar
Mirabet V, Das P, Boudaoud A, Hamant O. The role of mechanical forces in plant morphogenesis. Annu Rev Plant Biol. 2011; 62:365–85.
Article
CAS
PubMed
Google Scholar
Lee AB, Mumford D, Huang J. Occlusion models for natural images: A statistical study of a scale-invariant dead leaves model. International Journal of Computer Vision. 2001; 41:35–59.
Article
Google Scholar
Bordenave C, Gousseau Y, Roueff F. The dead leaves model: A general tessellation modeling occlusion. Adv Appl Probability. 2006; 38:31–46.
Article
Google Scholar
Gousseau Y, Roueff F. Modeling occlusion and scaling in natural images. SIAM Journal of Multiscale Modeling and Simulation. 2007; 6:105–34.
Article
Google Scholar
Langhans M, Meckel T. Single-molecule detection and tracking in plants. Protoplasma. 2014; 251(2):277–91.
Article
CAS
PubMed
Google Scholar
Elgass K, Caesar K, Schleifenbaum F, Stierhof Y-D, Meixner AJ, Harter K. Novel application of fluorescence lifetime and fluorescence microscopy enables quantitative access to subcellular dynamics in plant cells. PLoS One. 2009; 4(5):5716.
Article
Google Scholar
Gutierrez R, Grossmann G, Frommer WB, Ehrhardt DW. Opportunities to explore plant membrane organization with super-resolution microscopy. Plant Physiol. 2010; 154(2):463–6.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sparkes I, Graumann K, Martinière A, Schoberer J, Wang P, Osterrieder A. Bleach it, switch it, bounce it, pull it: using lasers to reveal plant cell dynamics. J Exp Bot. 2010:351. doi:10.1093/jxb/erq351.
Fitzgibbon J, Bell K, King E, Oparka K. Super-resolution imaging of plasmodesmata using three-dimensional structured illumination microscopy. Plant Physiol. 2010; 153(4):1453–63.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wan Y, Ash WM, Fan L, Hao H, Kim MK, Lin J. Variable-angle total internal reflection fluorescence microscopy of intact cells of Arabidopsis thaliana. Plant Methods. 2011; 7(1):27.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cloetens P, Mache R, Schlenker M, Lerbs-Mache S. Quantitative phase tomography of Arabidopsis seeds reveals intercellular void network. Proc Nat Acad Sci USA. 2006; 103(39):14626–30.
Article
PubMed Central
CAS
PubMed
Google Scholar
Costa A, Candeo A, Fieramonti L, Valentini G, Bassi A. Calcium dynamics in root cells of Arabidopsis thaliana visualized with selective plane illumination microscopy. PLoS ONE. 2013; 8:75646.
Article
Google Scholar
Fernandez R, Das P, Mirabet V, Moscardi E, Traas J, Verdeil J, et al. Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution. Nat Methods. 2010; 7:547–53.
Article
CAS
PubMed
Google Scholar
Leea K, Avondob J, Morrisonc H, Blotb L, Starkd M, Sharpec J, et al. Visualizing plant development and gene expression in three dimensions using optical projection tomography. Plant Cell. 2006; 18:2145–56.
Article
Google Scholar
Mairhofer S, Zappala S, Tracy SR, Sturrock C, Bennett M, Mooney SJ, et al. RooTrak: automated recovery of three-dimensional plant root architecture in soil from X-ray microcomputed tomography images using visual tracking. Plant Physiol. 2012; 158(2):561–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zappala S, Mairhofer S, Tracy S, Sturrock CJ, Bennett M, Pridmore T, et al. Quantifying the effect of soil moisture content on segmenting root system architecture in X-ray computed tomography images. Plant and Soil. 2013; 370(1-2):35–45.
Article
CAS
Google Scholar
Mairhofer S, Zappala S, Tracy S, Sturrock C, Bennett MJ, Mooney SJ, et al. Recovering complete plant root system architectures from soil via X-ray micro-computed tomography. Plant Methods. 2013; 9(8):1–7.
Google Scholar
Salon C, Jeudy C, Bernard C, Mougel C, Coffin A, Bourion V, et al. Google Patents. EP Patent App. 2014:EP20,130,173,626. http://www.google.com/patents/EP2679088A1?cl=fr.
Dinneny JR. Luciferase Reporter System for Roots and Methods of Using the Same. Google Patents. US Patent App. 2014; 13/970:960. http://www.google.com/patents/US20140051101.
Google Scholar
Rellán Álvarez R. Growth and luminescence observatory for roots (glo-roots): A platform for the analysis of root structure and physiology in soil. In: Plant and Animal Genome XXII Conference. Plant and Animal Genome: 2014.
Chéné Y, Belin E, Chapeau-Blondeau F, Boureau T, Caffier V, Rousseau D. Anatomo-functional bimodality imaging for plant phenotyping: An insight through depth imaging coupled to thermal imaging. In: Plant Image Analysis: Fundamentals and Applications. Boca Raton: CRC Press: 2014. Chap. 9.
Google Scholar
Paulus S, Behmann J, Mahlein A-K, Plümer L, Kuhlmann H. Low-cost 3d systems: Suitable tools for plant phenotyping. Sensors. 2014; 14(2):3001–18.
Article
PubMed Central
PubMed
Google Scholar
Jones HG, Vaughan RA. Remote Sensing of Vegetation: Principles, Techniques, and Applications. Oxford: Oxford University Press; 2010.
Google Scholar
Zarco-Tejada PJ, González-Dugo V, Berni JA. Fluorescence, temperature and narrow-band indices acquired from a UAV platform for water stress detection using a micro-hyperspectral imager and a thermal camera. Remote Sensing Environ. 2012; 117:322–37.
Article
Google Scholar
Hettinger JW, de la Pena Mattozzi M, Myers WR, Williams ME, Reeves A, Parsons RL, et al. Optical coherence microscopy. a technology for rapid, in vivo, non-destructive visualization of plants and plant cells. Plant Physiol. 2000; 123(1):3–16.
Article
PubMed Central
CAS
PubMed
Google Scholar
Meglinski I, Buranachai C, Terry L. Plant photonics: application of optical coherence tomography to monitor defects and rots in onion. Laser Phys Lett. 2010; 7(4):307.
Article
Google Scholar
Dhondt S, Wuyts N, Inzé D. Cell to whole-plant phenotyping: the best is yet to come. Trends Plant Sci. 2013; 18(8):428–39.
Article
CAS
PubMed
Google Scholar
Ehrhardt DW, Frommer WB. New technologies for 21st century plant science. The Plant Cell Online. 2012; 24(2):374–94.
Article
CAS
Google Scholar
Sozzani R, Busch W, Spalding EP, Benfey PN. Advanced imaging techniques for the study of plant growth and development. Trends in Plant Sci. 2014; 19(5):304–10.
Article
CAS
Google Scholar
Benoit L, Belin É, Durr C, Chapeau-Blondeau F, Demilly D, Ducournau S, et al. Computer vision under inactinic light for hypocotyl-radicle separation with a generic gravitropism-based criterion. Comput Electron Agric. 2015; 111:12–7.
Article
Google Scholar
Bell K, Mitchell S, Paultre D, Posch M, Oparka K. Correlative imaging of fluorescent proteins in resin-embedded plant material1. Plant Physiol. 2013; 161(4):1595–603.
Article
PubMed Central
CAS
PubMed
Google Scholar
Jahnke S, Menzel MI, Van Dusschoten D, Roeb GW, Bühler J, Minwuyelet S, et al. Combined mri–pet dissects dynamic changes in plant structures and functions. The Plant J. 2009; 59(4):634–44.
Article
CAS
Google Scholar
Zitova B, Flusser J. Image registration methods: a survey. Image Vision Comput. 2003; 21(11):977–1000.
Article
Google Scholar
Lowe DG. Distinctive image features from scale-invariant keypoints. Int J Comput Vision. 2004; 60(2):91–110.
Article
Google Scholar
Dale MRT, Mah M. The use of wavelets for spatial pattern analysis in ecology. Journal of Vegetation Science. 1998; 9(6):805–14.
Article
Google Scholar
Gu X, Du J-X, Wang X-F. Leaf recognition based on the combination of wavelet transform and Gaussian interpolation. In: Advances In Intelligent Computing. Berlin: Springer: 2005. p. 253–62.
Google Scholar
Prasad S, Kumar P, Tripathi R. Plant leaf species identification using curvelet transform. In: 2nd International Conference on Computer and Communication Technology (ICCCT). IEEE: 2011. p. 646–52.
Casanova D, de Mesquita Sa Junior JJ, Martinez Bruno O. Plant leaf identification using Gabor wavelets. Int J Imaging Sys Technol. 2009; 19(3):236–43.
Article
Google Scholar
Bours R, Muthuraman M, Bouwmeester H, van der Krol A. Oscillator: A system for analysis of diurnal leaf growth using infrared photography combined with wavelet transformation. Plant Methods. 2012; 8(1):29.
Article
PubMed Central
PubMed
Google Scholar
Epinat V, Stein A, de Jong SM, Bouma J. A wavelet characterization of high-resolution NDVI patterns for precision agriculture. Int J Appl Earth Observation Geoinformation. 2001; 3(2):121–32.
Article
Google Scholar
Strand EK, Smith AM, Bunting SC, Vierling LA, Hann DB, Gessler PE. Wavelet estimation of plant spatial patterns in multitemporal aerial photography. Int J Remote Sensing. 2006; 27(10):2049–54.
Article
Google Scholar
Frangi AF, Niessen WJ, Vincken KL, Viergever MA. Multiscale vessel enhancement filtering. In: Medical Image Computing and Computer-Assisted Interventation-MICCAI’98. Berlin: Springer: 1998. p. 130–7.
Google Scholar
Sage D, Neumann FR, Hediger F, Gasser SM, Unser M. Automatic tracking of individual fluorescence particles: Application to the study of chromosome dynamics. IEEE Trans Image Process. 2005; 14:1372–83.
Article
PubMed
Google Scholar
Huang NE, Shen Z, Long SR, Wu MC, Shih HH, Zheng Q, et al. The empirical mode decomposition and the Hilbert spectrum for nonlinear and non-stationary time series analysis. Proc R Soc London Ser A: Math Phys Eng Sci. 1998; 454(1971):903–95.
Article
Google Scholar
Nunes JC, Bouaoune Y, Delechelle E, Niang O, Bunel P. Image analysis by bidimensional empirical mode decomposition. Image Vision Comput. 2003; 21(12):1019–26.
Article
Google Scholar
Nunes JC, Guyot S, Deléchelle E. Texture analysis based on local analysis of the bidimensional empirical mode decomposition. Machine Vision Appl. 2005; 16(3):177–88.
Article
Google Scholar
Myers WL, Patil GP. Pattern-Based Compression of Multi-Band Image Data for Landscape Analysis. Berlin: Springer; 2006.
Google Scholar
Buades A, Coll B, Morel J-M. A review of image denoising algorithms, with a new one. Multiscale Model Simul. 2005; 4(2):490–530.
Article
Google Scholar
Buades A, Coll B, Morel J-M. A non-local algorithm for image denoising. In: Computer Vision and Pattern Recognition, 2005. CVPR 2005. IEEE Computer Society Conference On. vol. 2. IEEE: 2005. p. 60–5.
Palmer MW. Fractal geometry: A tool for describing spatial patterns of plant communities. Vegetatio. 1988; 75:91–102.
Article
Google Scholar
Critten DL. Fractal dimension relationships and values associated with certain plant canopies. J Agric Eng Res. 1997; 67:61–72.
Article
Google Scholar
Alados CL, Escos J, Emlen JM, Freeman DC. Characterization of branch complexity by fractal analyses. Int J Plant Sci. 1999; 160:147–55.
Article
Google Scholar
Morávek Z, Fiala J. Fractal dynamics in the growth of root. Chaos, Solitons & Fractals. 2004; 19:31–4.
Article
Google Scholar
Alados CL, Pueyo Y, Navas D, Cabezudo B, Gonzalez A, Freeman DC. Fractal analysis of plant spatial patterns: A monitoring tool for vegetation transition shifts. Biodivers Conserv. 2005; 14:1453–68.
Article
Google Scholar
Ruderman DL, Bialek W. Statistics of natural images: Scaling in the woods. Phys Rev Lett. 1994; 73:814–7.
Article
PubMed
Google Scholar
Ruderman DL. Origins of scaling in natural images. Vision Res. 1997; 37(23):3385–98.
Article
CAS
PubMed
Google Scholar
Chauveau J, Rousseau D, Richard P, Chapeau-Blondeau F. Multifractal analysis of three-dimensional histogram from color images. Chaos, Solitons & Fractals. 2010; 43(1):57–67.
Article
Google Scholar
Chauveau J, Rousseau D, Chapeau-Blondeau F. Fractal capacity dimension of three-dimensional histogram from color images. Multidimensional Syst Signal Process. 2010; 21(2):197–211.
Article
Google Scholar
Chapeau-Blondeau F, Chauveau J, Rousseau D, Richard P. Fractal structure in the color distribution of natural images. Chaos, Solitons & Fractals. 2009; 42(1):472–82.
Article
Google Scholar
Chéné Y, Belin E, Rousseau D, Chapeau-Blondeau F. Multiscale analysis of depth images from natural scenes: Scaling in the depth of the woods. Chaos, Solitons & Fractals. 2013; 54:135–49.
Article
Google Scholar
Ferraro P, Godin C, Prusinkiewicz P. Toward a quantification of self-similarity in plants. Fractals. 2005; 13:91–109.
Article
Google Scholar
Martinez Bruno O, de Oliveira Plotze R, Falvo M, de Castro M. Fractal dimension applied to plant identification. Inf Sci. 2008; 178:2722–33.
Article
Google Scholar
Da Silva D, Boudon F, Godin C, Sinoquet H. Multiscale framework for modeling and analyzing light interception by trees. Multiscale Model Simul. 2008; 7:910–33.
Article
Google Scholar
Chéné Y, Rousseau D, Lucidarme P, Bertheloot J, Caffier V, Morel P, et al. On the use of depth camera for 3D phenotyping of entire plants. Comput Electron Agric. 2012; 82:122–7.
Article
Google Scholar
Chandra M, Rani M. Categorization of fractal plants. Chaos Solitons & Fractals. 2009; 41(3):1442–7.
Article
Google Scholar
Scheuring I, Riedi RH. Application of multifractals to the analysis of vegetation pattern. J Vegetation Sci. 1994; 5(4):489–496.
Article
Google Scholar
Bradshaw G, Spies TA. Characterizing canopy gap structure in forests using wavelet analysis. J Ecol. 1992; 80:205–15.
Article
Google Scholar
Tastumi J, Yamauchi A, Kono Y. Fractal analysis of plant root systems. Ann Bot. 1989; 64(5):499–503.
Google Scholar
Izumi Y, Iijima M. Fractal and multifractal analysis of cassava root system grown by the root-box method. Plant Production Sci. 2002; 5(2):146–51.
Article
Google Scholar
Ketipearachchi KW, Tatsumi J. Local fractal dimensions and multifractal analysis of the root system of legumes. Plant Production Sci. 2000; 3(3):289–95.
Article
Google Scholar