Xplo abstract¶

Improving our knowledge on plant architecture and development will help to answer remaining questions in ecology, agronomy and forestry, i.e. regarding plant acclimation and adaptation to changing environments or optimization of plant products. For this purpose, computational plants are becoming more and more popular and a lot of effort is made to build structural and functional models at the organ level in order to simulate plant growth and structure [1]. In this context, scientists need software to measure, analyse and model plant architectures.
The Xplo project has been developed in UMR AMAP since 2008 aiming at edition, visualization, exploration and simulation of plant architecture in a user-friendly manner. The software provides interactive tools to handle the plant structure topology (i.e. organ addition/ deletion) , geometry (i.e. 3D selection, edition, rotation) and dynamic (i.e. time line, scenarios). It has been used for various types of plant architecture studies (i.e Sunflower [2], Fir Sapling [3], Cecropia, Palm trees [4]).
Xplo is fully compatible with the multi-scale tree graphs (MTGs) data structure, which is commonly used to represent plant topology [5]. Users can explore this data structure to find or to improve hypotheses on plant development. Specific data can be extracted with combination of criteria and be visualised in tables and graphs. Simple analysis functions can be launched or data can be exported to external tools, i.e. AMAPMod, R or any other statistical computing environment, for more specific analyses. Once the model is designed, modellers can integrate their own plant simulation model to the platform and get benefit of its functionalities to test their hypotheses. Different scenarios can be computed for a growth model by interactively modifying model parameters or plant structure (i.e. by pruning) at defined time steps.
A plant geometry builder is integrated to Xplo. It allows a 3D plant mockup to be computed according to available geometrical data in the tree graph. If geometrical information is missing, standard default algorithms are provided to compute the missing data and to make 3D rendering available.
Xplo is an extensible software built according to the flexible Capsis methodology [6]. Independent simulation models are integrated in Xplo under the form of separated modules, and various tools can be plugged at any time using flexible extensions. This generic software can be run either in an interactive context with a multi-language graphical user interface or in script mode (Groovy/Python). Xplo is a free open-source software (LGPL) and is available on almost every OS.

REFERENCES

[1] Fourcaud, T., Zhang, XP., Stokes, A., Lambers, H., Koerner, C., 2008. Plant growth modelling and applications: The increasing importance of plant architecture in growth models. Annals of Botany, 101 : 1053-1063.
[2] Rey, H., Dauzat, J., Barczi, J.-F., Dosio, G., Chenu, K., Lecoeur, J., 2008. Using a 3-D virtual Sunflower to simulate light capture at organ, plant and plot levels: contribution of organ onterception, impact of heliotropism and analysis of genotypic differences. Annals of Botany, 101 (8) : 1139-1151. Conference associée : PMA06: The Second International Symposium on Plant Growth Modeling Simulation, Visualization and Applications.
[3] Taugourdeau, O., Dauzat, J., Griffon, S., de Coligny, F., Sabatier, S., Caraglio, Y., Barthélémy, D., 2010. Retrospective analysis of fir sapling growth vs. light interception In Proceedings of 6th International Workshop on Functional-Structural Plant Models (FSPM). S. l. : 93-95.6th International Workshop on Functional-Structural Plant Models (FSPM), 12-17/09/2010, University of California Davis, Etats-Unis.
[4] Mialet-Serra, I., Dauzat, J., Auclair, D., 2001. Using plant architectural models for estimation of radiation transfer in a coconut-based agroforestry system. Agroforestry Systems, 53 (2) : 141-149.
[5] Godin C., Caraglio Y., 1998. A multiscale model of plant topological structures, Journal of Theoretical Biology 191 : 1–46.
[6] de Coligny F., 2007. Efficient Building of Forestry Modelling Software with the Capsis Methodology. In: Fourcaud T, Zhang XP, eds. Plant Growth Modeling and Applications. Proceedings of PMA06. Los Alamitos, California: IEEE Computer Society, pp. 216-222.