M. Abera, P. Verboven, T. Defraeye, S. Fanta, M. Hertog et al., A plant cell division algorithm based on cell biomechanics and ellipse-fitting, Annals of Botany, vol.114, issue.4, pp.605-617, 2014.
DOI : 10.1093/aob/mcu078

R. Barillot, A. Escobar-gutiérrez, C. Fournier, P. Huynh, and D. Combes, Assessing the effects of architectural variations on light partitioning within virtual wheat-pea mixtures, Annals of Botany, vol.114, issue.4, pp.725-737, 2014.
DOI : 10.1093/aob/mcu099

URL : https://hal.archives-ouvertes.fr/hal-01095288

F. Boudon, C. Pradal, T. Cokelaer, P. Prusinkiewicz, and C. Godin, L-Py: An L-System Simulation Framework for Modeling Plant Architecture Development Based on a Dynamic Language, Frontiers in Plant Science, vol.3, p.76, 2012.
DOI : 10.3389/fpls.2012.00076

URL : https://hal.archives-ouvertes.fr/cirad-00703085

F. Boudon, C. Preuksakarn, P. Ferraro, J. Diener, P. Nacry et al., Quantitative assessment of automatic reconstructions of branching systems obtained from laser scanning, Annals of Botany, vol.114, issue.4, pp.853-862, 2014.
DOI : 10.1093/aob/mcu062

URL : https://hal.archives-ouvertes.fr/hal-01064917

G. Brunel, P. Borianne, G. Subsol, M. Jaeger, and Y. Caraglio, Automatic identification and characterization of radial files in light microscopy images of wood, Annals of Botany, vol.114, issue.4, pp.829-840, 2014.
DOI : 10.1093/aob/mcu119

URL : https://hal.archives-ouvertes.fr/hal-01076468

J. Butnor, J. Doolittle, L. Kress, S. Cohen, and K. Johnsen, Use of ground-penetrating radar to study tree roots in the southeastern United States, Tree Physiology, vol.21, issue.17, pp.1269-1278, 2001.
DOI : 10.1093/treephys/21.17.1269

. Carten?-`-fcarten?-`-carten?-`-f, F. Giannino, F. Schweingruber, and S. Mazzoleni, Modelling the development and arrangement of the primary vascular structure in plants, Annals of Botany, vol.114, issue.4, pp.619-627, 2014.
DOI : 10.1093/aob/mcu074

T. Chen, M. Henke, P. De-visser, G. Buck-sorlin, D. Wiechers et al., What is the most prominent factor limiting photosynthesis in different layers of a greenhouse cucumber canopy?, Annals of Botany, vol.114, issue.4, pp.677-688, 2014.
DOI : 10.1093/aob/mcu100

URL : https://hal.archives-ouvertes.fr/hal-01132281

D. Silva, D. Han, L. Faivre, R. Costes, and E. , Influence of the variation of geometrical and topological traits on light interception efficiency of apple trees: sensitivity analysis and metamodelling for ideotype definition, Annals of Botany, vol.114, issue.4, pp.739-752, 2014.
DOI : 10.1093/aob/mcu034

URL : https://hal.archives-ouvertes.fr/hal-01123080

D. Silva, D. Qin, L. Debuse, C. Dejong, and T. , Measuring and modelling seasonal patterns of carbohydrate storage and mobilization in the trunks and root crowns of peach trees, Annals of Botany, vol.114, issue.4, pp.643-652, 2014.
DOI : 10.1093/aob/mcu033

URL : https://hal.archives-ouvertes.fr/hal-01268912

H. Dale, A. Runions, D. Hobill, and P. Prusinkiewicz, Modelling biomechanics of bark patterning in grasstrees, Annals of Botany, vol.114, issue.4, pp.629-641, 2014.
DOI : 10.1093/aob/mcu156

J. Dauzat, B. Rapidel, and A. Berger, Simulation of leaf transpiration and sap flow in virtual plants: model description and application to a coffee plantation in Costa Rica, Agricultural and Forest Meteorology, vol.109, issue.2, pp.143-160, 2001.
DOI : 10.1016/S0168-1923(01)00236-2

T. Defraeye, D. Derome, P. Verboven, J. Carmeliet, and B. Nicolai, Cross-scale modelling of transpiration from stomata via the leaf boundary layer, Annals of Botany, vol.114, issue.4, pp.711-723, 2014.
DOI : 10.1093/aob/mct313

T. Dejong, D. Silva, D. Vos, J. Escobar-gutiérrez, and A. , Using functional-structural plant models to study, understand and integrate plant development and ecophysiology, Annals of Botany, vol.108, issue.6, pp.987-989, 2011.
DOI : 10.1093/aob/mcr257

T. Fourcaud, X. Zhang, A. Stokes, H. Lambers, and C. Körner, Plant Growth Modelling and Applications: The Increasing Importance of Plant Architecture in Growth Models, Annals of Botany, vol.101, issue.8, pp.1053-1063, 2008.
DOI : 10.1093/aob/mcn050

URL : https://hal.archives-ouvertes.fr/halsde-00281936

G. Garin, C. Fournier, B. Andrieu, V. Houlès, C. Robert et al., A modelling framework to simulate foliar fungal epidemics using functional-structural plant models, Annals of Botany, vol.114, issue.4, pp.795-812, 2014.
DOI : 10.1093/aob/mcu101

URL : https://hal.archives-ouvertes.fr/hal-01025689

C. Gigot, C. De-vallavieille-pope, L. Huber, and S. Saint-jean, Using virtual 3-D plant architecture to assess fungal pathogen splash dispersal in heterogeneous canopies: a case study with cultivar mixtures and a non-specialized disease causal agent, Annals of Botany, vol.114, issue.4, pp.863-875, 2014.
DOI : 10.1093/aob/mcu098

URL : https://hal.archives-ouvertes.fr/hal-01017748

C. Godin and Y. Caraglio, A Multiscale Model of Plant Topological Structures, Journal of Theoretical Biology, vol.191, issue.1, pp.1-46, 1998.
DOI : 10.1006/jtbi.1997.0561

URL : https://hal.archives-ouvertes.fr/hal-00827484

C. Godin and H. Sinoquet, Functional-structural plant modelling, New Phytologist, vol.166, issue.3, pp.705-708, 2005.
DOI : 10.1111/j.1469-8137.2005.01445.x

URL : https://hal.archives-ouvertes.fr/hal-01190931

C. Godin, E. Costes, and H. Sinoquet, A Method for Describing Plant Architecture which Integrates Topology and Geometry, Annals of Botany, vol.84, issue.3, pp.343-357, 1999.
DOI : 10.1006/anbo.1999.0923

URL : https://hal.archives-ouvertes.fr/hal-00827477

S. Griffon and F. De-coligny, AMAPstudio: An editing and simulation software suite for plants architecture modelling, Ecological Modelling, vol.290, 2014.
DOI : 10.1016/j.ecolmodel.2013.10.037

URL : https://hal.archives-ouvertes.fr/hal-01268810

S. Gu, J. Evers, L. Zhang, L. Mao, S. Zhang et al., Modelling the structural response of cotton plants to mepiquat chloride and population density, Annals of Botany, vol.114, issue.4, pp.877-887, 2014.
DOI : 10.1093/aob/mct309

J. Guillemot, N. Delpierre, P. Vallet, C. François, N. Martin-stpaul et al., Assessing the effects of management on forest growth across France: insights from a new functional-structural model, Annals of Botany, vol.114, issue.4, pp.779-793, 2014.
DOI : 10.1093/aob/mcu059

URL : https://hal.archives-ouvertes.fr/hal-01268996

T. Hakala, J. Suomalainen, S. Kaasalainen, and Y. Chen, Full waveform hyperspectral LiDAR for terrestrial laser scanning, Optics Express, vol.20, issue.7, pp.7119-7127, 2012.
DOI : 10.1364/OE.20.007119

J. Hanan and P. Prusinkiewicz, : Studying plants with functional???structural models, Functional Plant Biology, vol.35, issue.10, p.i? iii, 2008.
DOI : 10.1071/FPv35n10_FO

R. Hemmerling, O. Kniemeyer, D. Lanwert, W. Kurth, and G. Buck-sorlin, The rule-based language XL and the modelling environment GroIMP illustrated with simulated tree competition, Functional Plant Biology, vol.35, issue.10, pp.739-750, 2008.
DOI : 10.1071/FP08052

P. Minchin and A. Lacointe, New understanding on phloem physiology and possible consequences for modelling long-distance carbon transport, New Phytologist, vol.117, issue.3, pp.771-779, 2005.
DOI : 10.1111/j.1469-8137.2005.01323.x

URL : https://hal.archives-ouvertes.fr/hal-01190932

E. Nikinmaa, R. Sievänen, and T. Hölttä, Dynamics of leaf gas exchange, xylem and phloem transport, water potential and carbohydrate concentration in a realistic 3-D model tree crown, Annals of Botany, vol.114, issue.4, pp.653-666, 2014.
DOI : 10.1093/aob/mcu068

Y. Ong, K. Streit, M. Henke, and W. Kurth, An approach to multiscale modelling with graph grammars, Annals of Botany, vol.114, issue.4, pp.813-827, 2014.
DOI : 10.1093/aob/mcu155

C. Pradal, S. Dufour-kowalski, F. Boudon, C. Fournier, and C. Godin, OpenAlea: a visual programming and component-based software platform for plant modelling, Functional Plant Biology, vol.35, issue.10, pp.751-760, 2008.
DOI : 10.1071/FP08084

P. Prusinkiewicz, Modeling of spatial structure and development of plants: a review, Scientia Horticulturae, vol.74, issue.1-2, pp.113-149, 1998.
DOI : 10.1016/S0304-4238(98)00084-3

P. Prusinkiewicz, ART AND SCIENCE OF LIFE: DESIGNING AND GROWING VIRTUAL PLANTS WITH L-SYSTEMS, Acta Horticulturae, vol.630, issue.630, pp.15-28, 2004.
DOI : 10.17660/ActaHortic.2004.630.1

P. Prusinkiewicz, Modeling plant growth and development, Current Opinion in Plant Biology, vol.7, issue.1, pp.79-83, 2004.
DOI : 10.1016/j.pbi.2003.11.007

P. Prusinkiewicz and A. Lindenmayer, The algorithmic beauty of plants, 1990.
DOI : 10.1007/978-1-4613-8476-2

P. Prusinkiewicz and A. Runions, Computational models of plant development and form, New Phytologist, vol.56, issue.3, pp.549-569, 2012.
DOI : 10.1111/j.1469-8137.2011.04009.x

M. Renton and P. Poot, Simulation of the evolution of root water foraging strategies in dry and shallow soils, Annals of Botany, vol.114, issue.4, pp.763-778, 2014.
DOI : 10.1093/aob/mcu018

P. Room and H. J. , Virtual plants: new perspectives for ecologists, pathologists and agricultural scientists, Trends in Plant Science, vol.1, issue.1, pp.33-38, 1996.
DOI : 10.1016/S1360-1385(96)80021-5

R. Sievänen, E. Nikinmaa, P. Nygren, H. Ozier-lafontaine, J. Perttunen et al., Components of functional-structural tree models, Annals of Forest Science, vol.57, issue.5, pp.399-412, 2000.
DOI : 10.1051/forest:2000131

P. Stenberg, M. Mõttus, M. Rautiainen, and R. Sievänen, Quantitative characterization of clumping in Scots pine crowns, Annals of Botany, vol.114, issue.4, pp.689-694, 2014.
DOI : 10.1093/aob/mct310

M. Vandegehuchte, A. Guyot, M. Hubeau, D. Swaef, T. Lockington et al., Modelling reveals endogenous osmotic adaptation of storage tissue water potential as an important driver determining different stem diameter variation patterns in the mangrove species Avicennia marina and Rhizophora stylosa, Annals of Botany, vol.114, issue.4, pp.667-676, 2014.
DOI : 10.1093/aob/mct311

J. Wu and Y. Guo, An integrated method for quantifying root architecture of field-grown maize, Annals of Botany, vol.114, issue.4, pp.841-851, 2014.
DOI : 10.1093/aob/mcu009

M. Yang, P. Défossez, F. Danjon, and T. Fourcaud, Tree stability under wind: simulating uprooting with root breakage using a finite element method, Annals of Botany, vol.114, issue.4, pp.695-709, 2014.
DOI : 10.1093/aob/mcu122

T. Zenone, G. Morelli, and M. Teobaldelli, Preliminary use of ground-penetrating radar and electrical resistivity tomography to study tree roots in pine forests and poplar plantations, Functional Plant Biology, vol.35, issue.10, pp.1047-1058, 2008.
DOI : 10.1071/FP08062

J. Zhu, B. Andrieu, J. Vos, W. Van-der-werf, C. Fournier et al., Towards modelling the flexible timing of shoot development: simulation of maize organogenesis based on coordination within and between phytomers, Annals of Botany, vol.114, issue.4, pp.753-762, 2014.
DOI : 10.1093/aob/mcu051

URL : https://hal.archives-ouvertes.fr/hal-01096700

M. Zimmermann, Xylem structure and the ascent of sap, 1983.
DOI : 10.1007/978-3-662-22627-8