• AgroDeep Doc

    Documentation d'AgroDeep

    git clone
  • Annotator

    IJ plugin for multi-class annotation of color images

  • Checker

    ImageJ plugin for the visual checking of True Positives, False Positives and False Negatives in AgroDeep studies

  • AMAP Tutorials

    This project gathers together computer science tutorials given at AMAP by people from AMAP and for AMAP people.

  • AMAPSim

    Simulation du développement architectural d'une plante

  • AMAPstudio

    AMAPstudio is a software suite for plants architecture modelling

    It contains several libraries:

    • Jeeb (Just Enough Elements for plants Biomodelling): a multi-purpose library by the AMAP developers
    • Sketch: a library for rough and flexible 3D rendering...
    • Simeo

      Scene Implantation Manager with Edition by Outline

      The tool is a multi purpose 3D scene editor to (i) create 3D scenes, (ii) export to rendering or other simulation tools, (iii) run scene level 3D evolution models....

    • Xplo

      A software for plant architecture eXploration

      Build, edit, visualize and filter plant architecture data. Handle simulation and modelisation modules. See the wiki Xplo for more details on the project....

  • DiagARCHI

    Application mobile pour du diagnostic architectural

    La méthode ARCHI est une méthode de diagnostic du dépérissement et des capacités de résilience des arbres basée sur des connaissances en architecture végétale. L’appli DiagARCHI est une aide au diagnostic, à la saisie des données in situ et aux statistiques au niveau d’une placette. L’observateur est guidé par un enchaînement de questions simples. Les questions concernent les symptômes de dégradation et les processus de restauration du houppier....

  • Java utils

    Common classes to all Archimed related projects


    BIOMASS, Estimating Aboveground Biomass and Its Uncertainty in Tropical Forests.

  • PlantBioM

    The goal of this project is to develop and provide a Scilab toolbox and a Java library devoted to the modelling and simulation of retroactions between plant growth and plant biomechanics

  • Capsis

    Computer-Aided Projection of Strategies In Silviculture

    Capsis is a simulation platform for forestry growth / dynamics models. It is a tool for forest scientists, forest managers and education. It has been developed in the AMAP laboratory since 1999....

  • CMMP

    Continuous Mathematical Models for Plants

    This reposotory gathers different source codes that are focused on the resolution of continuous mathematical models for plants. Those models are based on partial differential equations. Many efforts have been done toward the resolution of the time dependent advection-reaction-diffusion equation, and secondly toward the estimations of parameters in such a kind of equations. This equation appears in the C-Root models that aims at simulating complex root system growth in an aggregated way and for any plants. Thanks to this genericity, that is obtained at the price of the parameter estimation, the C-Root formalism could be extended to the modeling of a plant as a whole or the modeling of groups of plants. ...

    • CROOT

      CRoot dedicated project, by Emilie Peynaud

      This code, written in C++, solves the C-Root model [Bonneu et al 2012] using finite difference methods combined with the operator splitting technique [Tillier, Bonneu, IEEE, 2012]. The code also computes unknown parameters of the model from data using the Levenberg-Marquardt algorithm. The code was originally developed by Tillier. The C-Root model is designed to simulate root systems growth. It is based on the time dependent advection-reaction-diffusion equation. ...


      The FEMROOT code developped by E. Peynaud is written in Fortran 90. It solves the C-Root model [Bonneu et al 2012] using discontinuous Galerkin finite element methods combined with the operator splitting technique [Peynaud, BIOMATH, 2018]. The C-Root model is designed to simulate root systems growth. It is based on the time dependent advection-reaction-diffusion equation. ...

    • PPE-PDE

      PPE-PDE project, by Emilie Peynaud

      The PPE-PDE project is written in Python. Its name stands for "Python Parameter Estimation in Partial Differential Equation". Is was developped in the framework of Laura Wamba Mackeng's master thesis project. The code computes estimations of some parameters of the C-Root model from synthetic data. The purpose of the work was to test basic methods like the least square method in simplified test cases. The C-Root model was designed to simulate root systems growth. It is based on the time dependent advection-reaction-diffusion equation. ...


    A set of tools dedicated to tropical forest ecology based on remote sensing data

    • AlloStand

      Convert tree inventories to 3D spatial mockups.


      From R command line :


      Source code

      git clone
    • AMAPVox

      AMAPVox, LiDAR data voxelisation software

      Copyright (c) (Institut de Recherche pour le Développement) 2016-2022



    • FOTO

      FOTO for FOurier transform Textural Ordination

      Predicting stand structure parameters for tropical forests from remotely sensed data by defining an index of canopy texture from the ordination of the Fourier spectra computed for tropical rain forest images....

  • MAIA

    Ressources MAIA

    Ateliers MAIA P3M

    Supports des ateliers sur le Wiki

    CR des réunions

    Compte rendu des réunions sur amap-collaboratif

  • Mimetic Point Process

    R package to generate mimetic point processes.

  • Pl@ntNet-Publish

    Botanical data Publication based on symphony

  • Pl@ntNet-Site vitrine

    Le projet du site vitrine, accessible à l'adresse
    et le site mobile

    svn checkout vitreplantnet
  • Repository for the network of central African forest plots

    This repository aim to host datasets extracted from the network of central African forest plots.

  • Toaster

    Tree and planT Organs And STructures analysER (TOASTER) is the ImageJ's plugin which manages the different tools developped by the lab for the identification and geometrical characterization of anatomical structures from macro or microscopic images....

    • GT-RootS

      GT-RootS (Global Traits of Root System) is the automated Java-based solution we develop for processing the root system images coming from the Rhizoscope, a Cirad’s phenotyping plateform dedicated to adult cereal plants.

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