## Projects

- AgroDeep Doc
Documentation d'AgroDeep

git clone http://amap-dev.cirad.fr/git/agrodeep-doc.git

- 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*

http://amapstudio.cirad.fr/soft/amapsim/start - AMAPstudio
*AMAPstudio is a software suite for plants architecture modelling*

http://amapstudio.cirad.fr/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*

http://amapstudio.cirad.fr/soft/simeo/startThe 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*

http://amapstudio.cirad.fr/soft/xplo/startBuild, 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*

https://amap.cirad.fr/fr/edite_projet.php?projet_id=73La 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
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*

https://capsis.cirad.fr/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. ...

- FEMROOT
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. ...

- FOREST-RS
*A set of tools dedicated to tropical forest ecology based on remote sensing data*- AMAPVox
# AMAPVox, LiDAR data voxelisation software¶

Copyright (c) https://www.ird.fr (Institut de Recherche pour le Développement) 2016-2022

## Reference¶

...

- 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....

- 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 www.plantnet-project.org

et le site mobile m.plantnet-project.org`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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