OpenAlea models, algorithms and simulation tools for Root Branching Network

The Colloquium is held in Paris, on 26 and 27 June 2025.

This repository share a 2D+t root system architecture (RSA) dataset reconstructed automatically from the HIRROS platform.

OpenAlea is an open-source platform for branchingnetwork Tutorial for the workshop on Branching Networks

OpenAlea provides a set of packages for working on plant architecture

• Mutliscale Tree Graph or MTG is a standard datastructure for querying, analysing, and visualising Plant Arhitecture.
• RSML is a format for representing Root System Architecture
• LPy is a language and a (L-)system to simulate plants in 3D
• Hydroroot computes hydraulic fluxes in a root architecture
• StructureAnalysis provides models for statistical analysis of the structure of the plants (Markov, Semi-Markov, Hidden-Semi_Markov models for sequence and tree)
• and much more (see https://github.com/openalea and https://github.com/openalea-incubator)

RootSystemTracker reconstructs RSA from 2D+t images and

Authors

• Christophe Pradal (@pradal ) : Multiscale Tree Graph, Topological Analysis, Simulation, Software
• Fabrice Bauget (@baugetfa) : Hydraulic, RSML, Software
• Thomas Arsouze (@thomasarsouze) : software
• Frederic Boudon (@fredboudon): L-System Simulation, Tree Matching
• Jean-Baptiste Durand (@jbdurand) : Tree Markovian models, Structure Analysis
• Stathis Delivorias (@jazzsta) : Topological Data Analysis
• Romain Fernandez (@rocsg) : Spatio-temporal image analysis and phenotyping
• Loaï Gandeel (@Money-eng) : Spatio-temporal image analysis and phenotyping, RSML
• Philippe Nacry (INRAE, IPSIM) : HIRROS, data acquisition

Institute

• CIRAD, UMR AGAP institute and UMR AMAP.
• The MaCS4Plants network : Math & CS for modelling agroecosystems.
• INRAE IPSIM, Montpellier : hydraulic and root phenotyping
• inria and INRAE are members of the OpenAlea consortium

Install

Dependencies

Packages are on the openalea3 channel

Dependencies :

• openalea.mtg
• openalea.plantgl
• rsml

Mamba / Conda

mamba create -n branch -c openalea3 -c conda-forge openalea.mtg oawidgets rsml networkx jupyterlab

To compute fluxes use

mamba activate branch
mamba install -c openalea3 -c conda-forge openalea.hydroroot

Citations

Multiscale plat and root representation

• Pradal, C., & Godin, C. (2020). MTG as a standard representation of plants in FSPMs.
• Lobet, G., Pound, M. P., Diener, J., Pradal, C. et al. (2015). Root system markup language: toward a unified root architecture description language. Plant physiology, 167(3), 617-627. https://doi.org/10.1104/pp.114.253625

Root Hydraulic Architecture

• Bauget, F., Protto, V., Pradal, C., Boursiac, Y., & Maurel, C. (2023). A root functional–structural model allows assessment of the effects of water deficit on water and solute transport parameters. Journal of Experimental Botany, 74(5), 1594-1608. https://doi.org/10.1093/jxb/erac471
• Boursiac, Y., Pradal, C., Bauget, F., Lucas, M., Delivorias, S., Godin, C., & Maurel, C. (2022). Phenotyping and modeling of root hydraulic architecture reveal critical determinants of axial water transport. Plant Physiology, 190(2), 1289-1306. https://doi.org/10.1093/plphys/kiac281

Plant Simulation with L-Systems

• Boudon, F., Pradal, C., Cokelaer, T., Prusinkiewicz, P., & Godin, C. (2012). L-Py: an L-system simulation framework for modeling plant architecture development based on a dynamic language. Frontiers in plant science, 3, 76. https://doi.org/10.3389/fpls.2012.00076

Statistical Analysis of branching systems

• Hidden Markov Tree Models : Durand et al., 2004, 2005
• Partially ordered Markov out-trees : Fernique 2014

Contributors

Thanks to all that ontribute making this package what it is !