Agropolis computational plant seminar

Participants : Yann Guédon, Thierry Fourcaud [CIRAD, AMAP] , Christine Granier [INRA, LEPSE] , Soazig Guyomarc'H [Montpellier 2 University, DIADE] , Laurent Laplaze [IRD, DIADE] .

Funding: Agropolis foundation (Contractor for Virtual Plants: CIRAD. From 2013 to 2016)

In the context of the creation of a world-level pole on plant science in the region Languedoc-Roussillon, we created a monthly seminar on plant modeling and its applications. The seminar is organized by Yann Guédon, Thierry Fourcaud (CIRAD, AMAP), Christine Granier (INRA, LESPE), Soazig Guyomarc'h (Montpellier 2 University, DIADE) and Laurent Laplaze (IRD, DIADE) with the support of Agropolis International and Agropolis Foundation. In 2015, we organized a two-day workshop devoted to the modeling of plant development from the cellular to the organ scale.

MecaFruit3D

Participants : Mik Cieslak, Frédéric Boudon, Christophe Godin, Nadia Bertin [PSH, Avignon] .

Funding: Labex Agro (Contractor for Virtual Plants: INRA, from 2013 to 2016)

The fruit cuticle plays a major role in fruit development and shelf-life. It is involved in water losses, cracking, and protection against stress, and thus it may have major economic impacts. Objectives of the project are to better understand the multiple roles of the fruit cuticle in the control of fleshy fruit growth and quality.

Integrated model of plant organ growth

Participants : Yann Guédon, Christine Granier [INRA, LEPSE] , Garance Koch [INRA, LEPSE] , Nadia Bertin [INRA, PSH] , Valentina Baldazzi [INRA, PSH] .

Funding: Labex Agro (Contractor for Virtual Plants: CIRAD. From 2015 to 2018)

The objective of this project is to develop a generic model which will predict interactions among the main processes controlling the development of source and sink organs in tomato, i.e. cell division, cell expansion and endoreduplication in relation to carbon and water fluxes under fluctuating environment. To achieve this objective we will i) capitalize on expertise, multi-scale phenotyping tools and genetic resources already compiled on the fruit model tomato and the model plant Arabidopsis thaliana; ii) perform new experiments to collect phenotyping data currently missing in this field, especially concerning the early phase of fruit and leaf development in tomato and the interactions between genes and environment; iii) develop a process-based model of organ growth which will integrate knowledge collected at the different scales.

Partners: PSH, INRA, Avignon; LEPSE, INRA, Montpellier, Biologie du fruit et Pathologie INRA, Bordeaux;

SegmentationEvaluation

Participants : Sophie Ribes, Benjamin Gilles [LIRMM] , Guillaume Baty, Alizon Konig, Guillaume Cerutti.

Funding: IBC (Contractor for Virtual Plants: UM, 2015)

The goal of this project is to develop a framework allowing a robust validation for image segmentation. Segmentation is an ill-posed problem, and conventional validation approaches are corrupted by both intra and inter observer variabilities. We plan to develop: efficient tools allowing a creation of gold standard segmentation data (Alizon Konig, master internship under the supervision of Sophie Ribes); robust metrics to quantify differences between ground truth and algorithmic results.

Partners: ICAR, LIRMM, Montpellier.