Section: Software

V-Plants

Participants : Frédéric Boudon, Christophe Godin, Yann Guédon, Christophe Pradal [ coordinator ] , Daniel Barbeau, Florence Chaubert-Pereira, Jérôme Chopard, Thomas Cokelaer, David Da Silva, Jean-Baptiste Durand, Pascal Ferraro, Eric Moscardi, Szymon Stoma.

Other participant: Aida Ouangraoua (LaBRI, Bordeaux).

Computer algorithms and tools developed by the Virtual Plants team are integrated in a common software suite V-Plants , dedicated to the modeling and analysis of plant development at different scales (e.g. cellular tissue, whole plant, stand). The VPlants packages are integrated in OpenAlea as Python components.

In 2009, the V-Plants packages have been integrated as components of the OpenAlea platform (see Section 5.2 ). Several components are distributed and usable through the visual programming environment (see figure 2 ):

• Multi-scale geometric modelling and visualisation. VPlants.PlantGL is a geometric library which provides a set of graphical tools and algorithms for 3D plant modelling at different scales [15] . It is used by many other components to represent the geometry of biological shapes from 3D meristems, plant architectures to plant populations. VPlants.PlantGL is built around a scene-graph datastructure and provides efficient algorithms and original geometrical shapes (parametric surfaces, dedicated envelops) useful for plant modeling.

• Statistical sequence and tree analysis. Different statistical packages (i.e. VPlants.StatTool, VPlants.SequenceAnalysis, VPlants.TreeMatching and VPlants.TreeAnalysis) are available into OpenAlea. They provide different models and algorithms for plant architecture analysis and simulation.

• Meristem functioning and development. A first set of components has been created in the last 4-years period to model meristem development in OpenAlea. These tools are currently being integrated thoroughly in the platform so that modelers and biologists can use them, and reuse components easily (for meristem 3D reconstruction, cell tracking, statistical analysis of tissues, creating and manipulating atlases, creating or loading models of growth that can further be run on digitized structures, etc.

• Standard data structure for plant and tissue. OpenAlea.Container and OpenAlea.MTG are two packages which implement generic graph data structure to represent the topological structure of the meristem and of the plant architecture, as well as the dataflow graph in OpenAlea. These components make it possible to share plant representations between users and fosters the interoperability of new models.

• Simulation system. The L-Py package couples the well known L-system formalism for simulating fractal structures and plant development with the Python modeling language (basis of OpenAlea). Extensions to integrate multiscale models are currently being developed in collaboration with P. Prusinkiewicz and his team from the University of Calgary.

Figure 1. V-Plants components of the OpenAlea platform: simulating plant processes at different scales. Top Left: Reconstruction of a virtual meristem, analysis and simulation of the auxin fluxes inside the meristem. Top Right: Reconstruction of a virtual apple tree from digitized data. Bottom: Simulation of an ecosystem (A beech “Fagus Sylvatica L. ” trees forest) with a multi level approaches. On the left, explicit representation of the crown volumes that serves as input to generate the detailed representation, on the right.