Packages


Modelling with OpenAlea

MTG

https://readthedocs.org/projects/mtg/badge/?version=latest

Multiscale Tree Graph datastructure and interfaces

../_images/mtg_plantframe.png

MTG package aims to define :

  • A share data structure for plant architecture representation.

  • Read and write MTG files.

  • Export to various graph format.

  • Several algorithms for MTG.

Authors : Christophe Pradal, Christophe Godin

Institutes : Cirad, Inria

Source Code : Github

L-Py

https://readthedocs.org/projects/lpy/badge/?version=latest

Plant simulation using Lindenmayer Systems with Python

../_images/lpy_lpymagic.png

L-systems were conceived as a mathematical framework for modeling growth of plants. L-Py is a simulation software that mixes L-systems construction with the Python high-level modeling language.

Authors : Frédéric Boudon, Christophe Pradal, Thomas Cokelaer, Przemyslaw Prusinkiewicz, Christophe Godin

Institutes : Cirad, Inria, U. Calgary

Citation : Boudon et al., 2012, https://doi.org/10.3389/fpls.2012.00076

Source Code : Github

PlantGL

https://readthedocs.org/projects/plantgl-cpl/badge/?version=latest

An open-source graphic toolkit for the creation, simulation and analysis of 3D virtual plants

../_images/plantgl.png

Authors: Frédéric Boudon, Christophe Pradal, Christophe Nouguier, Jérôme Chopard, Christophe Godin

Institutes : Cirad, Inria

Citation : Pradal, Boudon et al., 2009, https://doi.org/10.1016/j.gmod.2008.10.001

Source Code : Github

OpenAlea Framework

Documentation status

OpenAlea Framework is able to discover and manage packages and logical components, build and evaluate dataflows and Generate final applications

../_images/openalea_web.png

Authors : Christophe Pradal, Samuel Dufour-Kowalski, Frédéric Boudon, Christian Fournier, Christophe Godin

Institutes : Cirad, Inria, INRA

Citation : Pradal et al., 2008, https://doi.org/10.1071/FP08084

Source Code : Github

VisuAlea

An application that allows to use OpenAlea packages and to build dataflow graphically

../_images/visualea_workflow.png

Authors : Christophe Pradal, Samuel

Institutes : Cirad, Inria

Source Code : Github




Plant Models

WeberPenn

An extension of the Weber & Penn model for OpenAlea

../_images/weberpenn_treegraph.png

Authors : Christophe Pradal

Institutes : Cirad

Original Article : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.380.2046

Source Code : Github


Plant Biophysics

Hydroshoot

https://readthedocs.org/projects/hydroshoot/badge/?version=latest

Hydroshoot model for 3D hydraulic architecture simulation

../_images/hydroshoot_grapevine.png

HydroShoot is a functional-structural plant modelling package taking into account hydraulic architecture and leaves energy budget and gas exchange.

Authors : Rami Albasha, Christian Fournier, Christophe Pradal

Institutes : INRA, Cirad

Citation : Albasha et al., 2019, https://doi.org/10.1093/insilicoplants/diz007

Source Code : Github

Phenotyping

Phenomenal

Documentation Status https://zenodo.org/badge/DOI/10.5281/zenodo.1436634.svg

3D reconstruction from high-throughput plant phenotyping images

../_images/phenomenal.png

Plant high-throughput phenotyping aims at capturing the genetic variability of plant response to environmental factors for thousands of plants, hence identifying heritable traits for genomic selection and predicting the genetic values of allelic combinations in different environments.

Authors : Simon Artzet, Christian Fournier, Christophe Pradal, Nicolas Brichet, Jerome Chopard, Michael Mielewczik

Institutes : INRA, Cirad

Source Code : Github

EarTrack

Documentation Status https://zenodo.org/badge/DOI/10.5281/zenodo.1002155.svg

EarTrack is an imaging library to detect and track future position of ears on maize plants

../_images/eartrack.png

Authors : Nicolas Brichet, Christian Fournier, Simon Artzet, Christophe Pradal,

Institutes : INRA, Cirad

Citation : Brichet et al., 2017, https://doi.org/10.1186/s13007-017-0246-7

Source Code : Github

Strawberry

https://readthedocs.org/projects/strawberry/badge/?version=latest

Strawberry architecture and visualization

../_images/strawberry.png

Strawberry package enables :

  • Analyses on strawberry architecture at several levels.

  • Modelize strawberry in 2 or 3d.

Authors : Marc Labadie, Christophe Pradal, Gaetan Heidsieck

Institutes : Cirad, Inria

Source Code : Github