B. Adam, H. Sinoquet, and C. Godin, 3A version 1.0 : Un logiciel pour l'Acquisition de l'Architecture des Arbres, intégrant la saisie simultanée de la topologie au format AMAPmod et de la géométrie par digitalisation 3D, Guide de l'utilisateur, 1999.

R. K. Ahuja, T. L. Magnanti, and J. B. Orlin, Network flows

. Theory, P. Applications, and . Hall, , 1993.

J. P. André, A study of vascular organization of Bamboos (Poaceae-Bambuseae) using a microcasting method, IAWA Journal, vol.19, pp.265-278, 1998.

A. Arneodo, F. Argoul, E. Bacry, J. Elezgaray, and J. F. Muzy, Ondelettes, multifractales et turbulences -de l'ADN aux croissances cristallines, Diderot Editeur, 1995.

J. M. Audergon, P. Monestiez, and R. Habib, Spatial dependences and sampling in a fruit tree: a new concept for spatial prediction in fruit studies, J. Horticult. Sci, vol.68, pp.99-112, 1993.
URL : https://hal.archives-ouvertes.fr/hal-02703894

C. J. Baker, The development of a theoretical model for the windthrow of plants, J. Theor. Biol, vol.175, pp.355-372, 1995.

F. Banegas, D. Michelucci, M. Roelens, and M. Jaeger,

F. Canovas, Hierarchical automated clustering of cloud point set by ellipsoidal skeleton, Application to organ geometric modeling from CT-scan images, SPIE's International Symposium on Medical Imaging, 1999.

J. F. Barczi, P. De-reffye, and Y. Caraglio, Essai sur l'identification et la mise en oeuvre des paramètres nécessaires à la simulation d'une architecture végétale : le logiciel AMAPsim, Modélisation et Simulation de l'Architecture des Végétaux, pp.205-254, 1997.

M. F. Barnsley, Fractals everywhere, 1988.

D. Barthélémy, C. Edelin, and F. Halle, Architectural concepts for tropical trees, Symposium on Tropical Forests, pp.89-100, 1989.

D. Barthélémy, C. Edelin, and F. Halle, Canopy architecture, pp.1-20, 1991.

A. D. Bell, The simulation of branching patterns in modular organisms, Phil. Trans. R. Soc. London, vol.313, pp.143-159, 1986.

A. D. Bell, Plant form, An illustrated guide to flowering plant morphology, 1991.

A. D. Bell, D. Roberts, and A. Smith, Branching patterns: the simulation of plant architecture, J. Theor. Biol, vol.81, pp.351-375, 1979.

N. Bertin, Environnement climatique, compétition pour les assimilats et modélisation de la nouaison de la tomate en culture sous serre, INRA, 1993.

P. Birnbaum, Modalités d'occupation de l'espace par les arbres en forêt guyanaise, 1997.

F. Blaise, Simulation du parallélisme dans la croissance des plantes et applications, 1991.

F. Blaise, J. F. Barczi, M. Jaeger, P. Dinouard, and P. De-reffye, Simulation of the growth of plants. Modeling of metamorphosis and spatial interactions in the architecture and development of plants, Cyberworlds, pp.81-109, 1998.

R. Borchert and H. Honda, Control of development in the bifurcating branch system of Tabeduia rosea: a computer simulation, vol.145, pp.184-195, 1985.

, Modélisation et simulation de l'architecture des végétaux, INRA Éditions, 1997.

Y. Caraglio and C. Edelin, Architecture et dynamique de la croissance du platane, Platanus hybrida Brot. (Platanaceae) {syn. Platanus acerifolia (Aiton) Willd.}, Bulletin de la Société Botanique de France, Lettres botaniques, vol.137, pp.279-291, 1990.

A. Cescatti, Modelling the radiative transfer in discontinuous canopies of asymmetric crowns. I. Model structure and algorithms, Ecol. Modell, vol.101, pp.263-274, 1997.

M. Chelle, Développement d'un modèle de radiosité mixte pour simuler la distribution du rayonnement dans les couverts végétaux, 1997.

S. G. Chen, R. Ceulemans, and I. Impens, A fractal-based Populus canopy structure model for the calculation of light interception, For. Ecol. Manag, vol.69, pp.97-110, 1994.

W. K. Chen, Applied graph theory, 1976.

C. Cluzeau, J. L. Dupouey, and B. Courbaud, Polyhedral representation of crown shape, A Geometric tool for growth modelling, Ann. Sci. For, vol.52, pp.297-306, 1995.
URL : https://hal.archives-ouvertes.fr/hal-00883000

E. Costes, H. Sinoquet, C. Godin, and J. J. Kelner, 3D digitizing based on tree topology: application to study the variability of apple quality within the canopy, Acta Horticulturae, 1999.
URL : https://hal.archives-ouvertes.fr/hal-02765689

C. Damez, Application de la méthode de radiosité aux simulations botaniques, Mémoire de DEA Imagerie, vision et Robotique, 1998.

F. Danjon, H. Sinoquet, C. Godin, F. Colin, and M. Drexhage, Characterisation of structural tree root architecture using 3D digitising and AMAPmod software, vol.211, pp.241-258, 1999.
URL : https://hal.archives-ouvertes.fr/hal-00827481

J. Dauzat, Colloque Structure du Couvert Végétal et Climat Lumineux: méthodes de caractérisation et applications, INRA Editions, pp.271-278, 1993.

J. Dauzat and M. N. Eroy, Simulating light regime and intercrop yields in coconut based farming systems, Eur. J. Agron, vol.7, pp.63-74, 1997.

J. Dauzat, B. Rapidel, and A. Berger, Simulation of leaf transpiration and sap flow in virtual plants: description of the model and application to a coffee plantation in Costa Rica, Agricult. For. Meteor, 1999.

P. De-reffye, P. Dinouard, and D. Barthélémy, Architecture et modélisation de l'Orme du Japon Zelkova serrata

. Makino, Ulmaceae): la notion d'axe de référence, De la forêt cultivée à l'industrie de demain, 3 e Colloque Sciences et Industries du Bois, Arbora, pp.351-352, 1990.

P. De-reffye, C. Edelin, J. Françon, M. Jaeger, and C. Puech, Plant models faithful to botanical structure and development, SIGGRAPH'88, pp.151-158, 1988.

P. De-reffye, T. Fourcaud, F. Blaise, and D. Barthélémy,

F. Houllier, A functional model of tree growth and tree architecture, vol.31, pp.297-311, 1997.

P. De-reffye, F. Houllier, F. Blaise, and T. Fourcaud, Essai sur les relations entre l'architecture d'un arbre et la grosseur de ses axes végétatifs, Modélisation et Simulation de l'Architecture des Végétaux, pp.255-423, 1997.

C. Deleuze and F. Houllier, A transport model for tree ring width, Silva Fenn, vol.31, pp.239-250, 1997.

O. Deussen, P. Hanrahan, B. Lintermann, and R. Mech,

M. Pharr and P. Prunsinkiewicz, Realistic modeling and rendering of plant ecosystems, SIGRAPPH'98, ACM, 1998.

A. J. Diggle, ROOTMAP-A model in three-dimensional coordinates of the growth and structure of fibrous root systems, Plant Soil, vol.105, pp.169-178, 1988.

C. Edelin, The monopodial architecture: the case of some trees species from tropical Asia, Research Pamph, p.105, 1990.

F. W. Ewers and P. Cruiziat, Measuring water transport and storage, Techniques and approaches in forest tree physiology, pp.91-115, 1991.
URL : https://hal.archives-ouvertes.fr/hal-02774301

K. Falconer, Fractal geometry: mathematical foundation and applications, 1990.

P. Ferraro and C. Godin, A distance measure between plant architectures, Ann. For. Sci, vol.57, pp.445-461, 2000.
URL : https://hal.archives-ouvertes.fr/hal-00883353

J. B. Fisher, How predictive are computer simulations of tree architecture?, Int. J. Plant Sci, vol.153, pp.137-146, 1992.

J. B. Fisher and C. L. Weeks, Tree architecture of Neea Nyctaginaceae: geometry and simulation of branches and the presence of two different models, Bull. Mus. Hist. Nat, vol.7, pp.385-401, 1985.

A. H. Fitter, The topology and geometry of plant root systems: influence of watering rate on root system topology in Trifolium pratense, Ann. Botany, vol.58, pp.91-101, 1986.

A. H. Fitter, An architectural approach to the comparative ecology of plant root systems, New Phytologist, vol.106, pp.61-77, 1987.

E. D. Ford, A. Avery, and R. Ford, Simulation of branch growth in the Pinaceae: interactions of morphology, phenology, foliage productivity, and the requirement for structural support, on the export of carbon, J. Theor. Biol, vol.146, pp.15-36, 1990.

T. Fourcaud, Analyse du comportement mécanique d'une plantes en croissance par la méthode des éléments finis, 1995.

T. Fourcaud and P. Lac, Mechanical analysis of the form and internal stresses of a growing tree by the finite element method, vol.77, pp.213-220, 1996.

T. Früh, Simulation of water flow in the branched tree architecture, Silva Fenn, vol.31, pp.275-285, 1997.

C. Godin and Y. Caraglio, A multiscale model of plant topological structures, J. Theor. Biol, vol.191, pp.1-46, 1998.
URL : https://hal.archives-ouvertes.fr/hal-00827484

C. Godin, E. Costes, and Y. Caraglio, Exploring plant topology structure with the AMAPmod software: an outline, Silva Fenn, vol.31, pp.355-366, 1997.

C. Godin, E. Costes, and H. Sinoquet, A method for describing plant architecture which integrates topology and geometry, Botany, vol.84, pp.343-357, 1999.
URL : https://hal.archives-ouvertes.fr/hal-00827477

C. Godin, Y. Guédon, and E. Costes, Exploration of plant architecture databases with the AMAPmod software illustrated on an apple-tree hybrid family, Agronomie, vol.19, pp.163-184, 1999.
URL : https://hal.archives-ouvertes.fr/hal-00827483

C. Godin, Y. Guédon, E. Costes, and Y. Caraglio, Plants to ecosystems -Advances in Computational Life Sciences, 2nd International Symposium on Computer Challenges in Life Science, pp.53-84, 1997.

M. Gondran and M. Minoux, Graphs and algorithms, 1984.
URL : https://hal.archives-ouvertes.fr/hal-01304880

J. F. Gouyet, Physique et structures fractales, 1992.

N. Greene, Voxel space automata: modeling with stochastic growth processing in voxel space, Comp. Graph, vol.23, pp.175-184, 1989.

F. Hallé, Modular growth in seed plants, Phil. Trans. R. Soc. London, vol.313, pp.77-87, 1986.

F. Hallé, R. A. Oldeman, and P. B. Tomlinson, Tropical trees and forests, An architectural analysis, 1978.

J. S. Hanan and P. M. Room, Plants to ecosystems -Advances in Computational Life Sciences, 2nd International Symposium on Computer Challenges in Life Science, pp.28-43, 1997.

J. L. Harper, B. R. Rosen, and J. White, The growth and form of modular organisms, 1986.

D. R. Hill, Object-oriented analysis and simulation, 1996.
URL : https://hal.archives-ouvertes.fr/hal-02077170

H. Honda, Description of the form of trees by the parameters of the tree-like body: Effects of the branching angle and the branch length on the shape of the tree-like body, J. Theor. Biol, vol.31, pp.331-338, 1971.

M. Jaeger, Représentation et simulation de la croissance des végétaux, 1987.

M. Jaeger, J. M. Leban, S. Chemouny, and L. Saint-andré, 3D stem reconstruction from CT scan exams, Biological improvement of wood properties, Third Workshop IUFRO WP S5, pp.1-04, 1999.

J. M. Janssen and A. Lindenmayer, Models for the control of branch positions and flowering sequences of capitula in Mycelis muralis (L.) Dumont (Compositae), New Phytologist, vol.105, pp.191-220, 1987.

R. S. Johnson and A. N. Lakso, Approaches to modeling light interception in orchards, HortScience, vol.26, pp.1002-1004, 1991.

C. Jourdan and H. Rey, Modelling and simulation of the architecture and development of the oil-palm (Elaeis guineensis Jacq.) root system. I. The model, Plant Soil, vol.190, pp.217-233, 1997.

T. Keisling and P. Counce, An encoding process for morphological analysis of soybean fruit distribution, Crop Sci, vol.37, pp.1665-1669, 1997.

W. Kurth, Growth grammar interpreter GROGRA 2.4: A software for the 3-dimentional interpretation of stochastic, sensitive growth grammar in the context of plant modelling, Introduction and Reference Manual, 1994.

W. Kurth, Morphological models of plant growth: possibilities and ecological relevance, Ecol. Modell, pp.299-308, 1994.

S. Ledizès, P. Cruiziat, A. Lacointe, H. Sinoquet, X. Leroux et al., A Model for simulating structure-function relationships in walnut tree growth processes, vol.31, pp.313-328, 1997.

P. Lewis, 3-D plant modelling for remote sensing simulation studies using the Botanical Plantb Modelling System, Agronomie, vol.19, pp.185-210, 1999.

H. B. Luck and J. Luck, Modélisation du fonctionnement d'un méristème par des L-systèmes et des systèmes de graphes et de cartes à réécriture parallèle, pp.375-395, 1987.

A. A. Mäkelä and R. P. Sievänen, Comparison of two shootroot partitioning models with respect to substrate utilization and functional balance, Ann. Botany, vol.59, pp.129-140, 1987.

B. B. Mandelbrot, The fractal geometry of nature, 1983.

B. B. Mandelbrot, Encyclopedia of physical science and technology, 1987.

R. E. Mcmurtrie, Forest productivity in relation to carbon partitioning and nutrient cycling: a mathematical model, pp.194-207, 1985.

K. J. Mitchell, Dynamics and simulated yield of Douglas-fir, For. Sci, vol.21, pp.1-39, 1975.

W. I. Newman, D. L. Turcotte, and A. M. Gabrielov, Fractal trees with side branching, Fractals, vol.5, pp.603-614, 1997.

E. Nikinmaa, Analyses of the growth of scots pine

, matching structure with function, Acta For. Fenn, vol.235, pp.3-68, 1992.

J. M. Norman and J. M. Welles, Radiative transfer in an array of canopies, Agronomy J, vol.75, pp.481-488, 1983.

L. Oosterhuis, R. A. Oldeman, and T. L. Sharik, Architectural approach to analysis of North American temperate deciduous forests, Canadian J. For. Res, vol.12, pp.835-847, 1982.

P. E. Oppenheimer, Real time design and animation of fractal plants and trees, SIG-GRAPH'86, ACM, pp.55-64, 1986.

L. Pagès, Root system architecture: from its represention to the study of its elaboration, Agromonie, vol.19, issue.4, pp.295-304, 1999.

J. Perttunen, R. Sievänen, E. Nikinmaa, H. Salminen, H. Saarenmaa et al., LIGNUM: a tree model based on simple structural units, Ann. Botany, vol.77, pp.87-98, 1996.

F. Preparata and R. Yeh, Introduction to discrete structures for computer science and engineering, 1973.

W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical recipes in C. The art of scientific computing, 1996.

P. Prusinkiewicz, Virtual Plant Laboratory. A hypertext document and software distribution, 1996.

P. Prusinkiewicz, Modeling of spatial structure and development of plants: a review, Scientia Horticult, vol.74, pp.113-149, 1998.

P. Prusinkiewicz, M. Hammel, J. Hanan, and R. Mech, Lsystem: from the theory to visual models of plants, Advances in Computational Life Sciences, I, CSIRO publishing, pp.1-27, 1997.

P. Prusinkiewicz and J. Hanan, Lindenmayer systems, fractals, and plants, 1989.

P. Prusinkiewicz, M. James, R. Mech, and . Synthetic-topiary, Computer Graphics Proceedings, pp.351-358, 1994.

P. Prusinkiewicz and A. Lindenmayer, The algorithmic beauty of plants, 1990.

P. Prusinkiewicz, W. R. Remphrey, and C. G. Davidson,

M. S. Hammel, Modeling the architecture of expanding Fraxinus pennsylvanica shoots using L-systems, Canadian J. Botany, vol.72, pp.701-714, 1994.

S. S. Rao, The finite element method in engineering, 1999.

W. R. Remphrey, B. R. Neal, and T. A. Steeves, The morphology and growth of Arctostaphylos uva-ursi bearberry: an architectural model simulating colonizing growth, Canadian J. Botany, vol.61, pp.2451-2458, 1983.

W. R. Remphrey and P. Prusinkiewicz, Quantification and modelling tree architecture, Advances in computational life sciences, vol.I, pp.45-52, 1997.

H. Rey, C. Godin, and Y. Guedon, Vers une représentation formelle des plantes, Modélisation et Simulation de l'Architecture des Végétaux, pp.139-171, 1997.

D. F. Robinson, A symoblic framework for the description of tree architecture models, Botan. J. Linn. Soc, vol.121, pp.243-261, 1996.

P. M. Room, L. Maillette, and J. S. Hanan, Module and metamer dynamics and virtual plants, Adv. Ecol. Res, vol.25, pp.105-157, 1994.

J. K. Ross, The radiation regim and the architecture of plant stands, 1981.

H. Salminen, H. Saarenmaa, J. Pertunen, R. Sievänen, J. Väkevä et al., Modelling trees using and object-oriented scheme, Math. Comp. Model, vol.20, pp.49-67, 1994.

H. Shimizu and R. D. Heins, Computer vision based system for plant growth analysis, Trans. ASAE, vol.38, pp.959-964, 1995.

K. Shinozaki, K. Yoda, K. Hozumi, and T. Kira, A quantitative analysis of plant. The Pipe Model theory I, Jpn. J. Ecol, vol.14, pp.97-105, 1964.

K. Shinozaki, K. Yoda, K. Hozumi, and T. Kira, A quantitative analysis of plant. The Pipe Model theory. I. Basic analyses, Jpn. J. Ecol, vol.14, pp.97-105, 1964.

F. X. Sillion, Hierarchical solution techniques for realistic rendering, State of the Art Report -Graphicon'95
URL : https://hal.archives-ouvertes.fr/inria-00510129

. Conférence, , 1995.

H. Sinoquet, B. Adam, P. Rivet, and C. Godin, Interactions between light and plant architecture in an agroforestry walnut tree, Agroforestry Forum, pp.37-40, 1998.
URL : https://hal.archives-ouvertes.fr/hal-00827486

H. Sinoquet and R. Bonhomme, Modeling raditive tranfer in mixed and row intercropping systems, Agricult. For. Meteor, vol.62, pp.219-240, 1992.

H. Sinoquet, P. Rivet, and C. Godin, Assessment of the three-dimensional architecture of walnut trees using digitising, Silva Fenn, vol.31, pp.265-273, 1997.

H. Sinoquet, S. Thanisawanyangkura, and H. Mabrouk,

P. Kasemsap, Characterisation of the light environment in canopies using 3D digitising and image processing, Ann. Botany, vol.82, pp.203-212, 1998.

A. R. Smith, Plants, fractals, and formal languages, Comp. Graph, vol.18, p.3, 1984.

G. S. Smith, J. P. Curtis, and C. M. Edwards, A Method for analysing plant Architecture as it relates to fruit quality using three-dimensional computer graphics, Ann. Botany, vol.70, pp.265-269, 1992.

J. S. Sperry, F. R. Adler, G. S. Campbell, and J. P. Comstock, Limitation of plant water use by rhizosphere and xylem conductance: results from a model, Plant Cell Environ, vol.21, pp.347-360, 1998.

A. Takenaka, A simulation model of tree architecture development based on growth response to local light environment, J. Plant Res, vol.107, pp.321-330, 1994.

R. E. Tarjan, Data structures and network algorithms, Society for Industrial and Applied Mathematics, 1983.

J. H. Thornley, A model to describe the partitioning of photosynthate during vegetative plant growth, Ann. Botany, vol.33, pp.419-430, 1969.

J. H. Thornley, A balanced quantitative model for root:shoot ratios in vegetative plants, Ann. Botany, vol.36, pp.431-441, 1972.

J. H. Thornley and I. R. Johnson, Plant and crop modeling: a mathematical approach to plant and crop physiology, 1990.

C. Tricot, Courbes et dimensions fractales, 1993.

M. T. Tyree and F. W. Ewers, The hydraulic architecture of trees and other woody plants, New Phytolology, vol.119, pp.345-360, 1991.

H. T. Valentine, Tree-growth models: dérivations employing the Pipe-model theory, J. Theor. Biol, vol.117, pp.579-585, 1985.

X. G. Viennot, G. Eyrolles, N. Janey, and D. Arquès, Combinatorial analysis of ramified patterns and computer imagery of trees, SIGGRAPH'89, ACM, pp.31-40, 1989.

C. E. Watson and F. M. Bourland, COTMAP, an interactive microcomputer program for mapping plant structure and fruiting patterns of cotton, Proceedings of the Beltwid Cotton Production Research Conferences, pp.131-134, 1989.

J. Weber and J. Penn, Creation and rendering of realistic trees, Computer Graphics Proceedings, Annual Conference Series, pp.381-394, 1995.

J. White, The plant as a metapopulation, Ann. Rev. Ecol. Syst, vol.10, pp.109-145, 1979.

B. Zeide, The state-of-the-art methodology of forest inventory, USDA Forest Service, pp.260-266, 1990.

B. Zeide, Fractal geometry in forestry applications, For. Ecol. Manag, vol.46, pp.179-188, 1991.

B. Zeide and P. Pfeifer, A methode for estimation of fractal dimension of tree crown, For. Sci, vol.37, pp.1253-1265, 1991.

M. H. Zimmermann, Hydraulic architecture of some diffuse-porous trees, Canadian J. Botany, vol.56, pp.2286-2295, 1978.