Team, Visitors, External Collaborators
Overall Objectives
Research Program
Highlights of the Year
New Software and Platforms
New Results
Partnerships and Cooperations
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Section: Partnerships and Cooperations

National Initiatives

Inria ADT - Gnomon

Participants : Olivier Ali, Romain Azaïs, Guillaume Cerutti, Florian Gacon, Christophe Godin, Jonathan Legrand, Grégoire Malandain [External Collaborator] , Teva Vernoux [External Collaborator] .

Gnomon is a user-friendly computer platform developed by the Mosaic team for seamless simulation of form development in silico. It is intended to be a major tool for the team members to develop, integrate and share their models, algorithms and tools. Flexible components (plugins) make it possible to up-load or to create such data-structures, to program their development, to analyze, visualize them and interact with them in 3D+time.

Based on the past experience of the team with the OpenAlea platform, the goal of this ADT is to develop a more scalable software engineering solution based on the dtk kernel developed by the group of software engineers (SED) from the Sophia-Antipolis Inria Center.


Inria IPL - Naviscope

Participants : Guillaume Cerutti, Emmanuel Faure [External Collaborator] , Christophe Godin, Jonathan Legrand, Grégoire Malandain [External Collaborator] .

In this project, we plan to develop original and cutting-edge visualization and navigation methods to assist scientists, enabling semi-automatic analysis, manipulation, and investigation of temporal series of multi-valued volumetric images, with a strong focus on live cell imaging and microscopy application domains. We will build Naviscope upon the strength of scientific visualization and machine learning methods in order to provide systems capable to assist the scientist to obtain a better understanding of massive amounts of information. Such systems will be able to recognize and highlight the most informative regions of the dataset by reducing the amount of information displayed and guiding the observer attention. Finally, we will overcome the technological challenge of gathering up the software developed in each team to provide a unique original tool for users in biological imaging, and potentially in medical imaging.

ANR - Imago (2016 - 2019)

Participants : Guillaume Cerutti, Christophe Godin, Jonathan Legrand.

The goal of this project is to investigate the role of ovule growth constraints on germ cell fate establishment. This project is motivated by recent findings from the partners’ groups suggesting that disturbances in cell divisions and expansion in early (pre-meiotic) ovules are sufficient to induce ectopic germ cells. These observations suggest novel routes to engineer apomixis in plants but remains poorly understood. Recent developments in high-resolution 3D imaging, image processing, and modeling offer a powerful combination of approaches to investigate this question. IMAGO proposes to elucidate patterning rules governing ovule growth, and their contribution to female germ cell fate acquisition. We use a combination of high-resolution static and real-time 3D imaging, quantitative image processing, cell-based growth models and functional approaches to (1) define cellular growth patterns in the ovule primordium using quantitative imaging (2) test patterning rules in silico by cell-based growth models (3) validate patterning rules in vivo using genetic, pharmacological and mechanical perturbations.


ANR DigEM (2015 - 2019)

Participants : Christophe Godin, Bruno Leggio, Patrick Lemaire [External Collaborator] , Grégoire Malandain [External Collaborator] .

In this project, we will use advanced ligh-sheet imaging of live embryos to quantitatively describe embryonic morphogenesis in ascidians, a class of animals that undergo very rapid genomic divergence, yet show an extraordinary stasis of embryonic morphologies, based on invariant early cell lineages shared by all studied species. The global aims of the proposal, which will bridge micro- and macroevolutionary scales of analysis, are: i) to provide a global systems-level description at cellular resolution of an animal embryonic program; ii) to use this description to characterize intra-specific and inter-specific patterns of morphogenetic variations; iii) to analyze possible molecular mechanisms explaining the unusual robustness of this program to environmental and genetic perturbations. To achieve these aims, we will combine advanced live light-sheet microscopy, computational biology, functional gene assays and evolutionary approaches.


ERA-CAPS Genes2shape (2018 - 2021)

Participants : Olivier Ali, Guillaume Cerutti, Christophe Godin, Bruno Leggio, Jan Traas [External Collaborator] .

This project is aimed at understanding how molecular regulation integrates with mechanics to control overall plant shape, an unresolved problem with wide implications for both fundamental and applied biology. We will address this issue in the Arabidopsis flower, which, besides their obvious importance as reproductive structures, are amongst the best characterised systems in plant developmental biology. From a mechanistic point of view, it is widely accepted that regulatory molecular networks interfere with the properties of the structural cellular elements (cell wall, cytoskeleton) to induce particular growth patterns. How this occurs and how this is coordinated in space is not known. To obtain a mechanistic understanding of such a complex process, information from multiple scales, from molecular networks to physical properties and geometry have to be combined into a single picture. An integrated tool to do so is currently not available. Building on our complementary experience in interdisciplinary research on plant development, we will therefore develop a tool, called the “Computable Flower” that permits (i) integration of data on geometry, gene expression and biomechanics and (ii) the user to explore, interpret and generate hypotheses based on data supported by mechanistic modelling approaches. The tool therefore provides an integrated description in the form of a 3D dynamic template of the growing flower bud.



Participant : Romain Azaïs.

The diving performance of lung-breathing vertebrates, such as seabirds, can be quantified using measurement devices equipped on animals that allow us to reconstruct their activity at sea. During a classic dive, diving animals are faced with a dilemma: on the one hand, they want to optimize the time spent in contact with prey and therefore increase the time spent in diving; but, on the other hand, they are forced to return to the surface to breathe and will want to minimize this duration which remains however constrained by physiological rules. In addition, the dives are gathered in sequences because the prey are generally grouped in patches. In this project, we propose to use specific mathematical models to understand the complexity of the multi-scale decision processes that condition not only the optimal duration of the dive but also dives within a bout and therefore the total duration of the bout.