Quantifying and modeling trajectories of living form development

In recent years, techniques to image the development of biological organisms have made spectacular progresses. Researchers are now able to observe the trajectories corresponding to the development of 3D- plant tissues or animal embryo with cellular resolution. The resulting data contain a diversity of informations including topology, geometry, molecular and physical properties of tissue parts, possibly at multiple scales. To organize the complexity of these data, first mathematical formalizations of these dynamic systems with dynamic structures (DS)2  have been developed and have progressively been identified as a new type of computational object whose geometry and bio-physical attributes change over time along with its topology. To work with these new computational objects and the corresponding imaging data, new tools and algorithms need be developed.

This PhD will address the question of quantifying, analyzing and modeling (DS)2 trajectories observed from live imaging at cellular resolution. First, based on previous work of the host team, the aim will be to quantify the growth (or change of shape) of the developing organism based on 3D time-lapse sequences of images obtained from confocal or light sheet microscopes. The work will then concentrate on the analysis of populations of observed 4D trajectories of (DS)2 and develop new conceptual ideas to characterize the variability of such objects. This project will mainly be carried out on plant tissue development in close connections with plant biologists, with possible applications to embryo development.

The host team, Mosaic, is an Inria project-team located in the Laboratoire Reproduction et Développement des Plantes (RDP) of the Ecole Normale Supérieure de Lyon (http://www.ens-lyon.fr/en), together offering a vibrant, international environment to study the fundamental principle of living form development. The team is made of mathematicians and computer scientists working in close collaboration with groups of biologists in France and abroad to address questions related to the understanding of form development in life sciences. This PhD program will take place in the context of a collaborative project, called Naviscope, gathering several teams at Inria working on related issues, and focussed on the development of concepts and tools to interpret living form development and functioning.

The candidate must have a Master degree in computer science, mathematics or physics. S/he should have skills in several of the following areas: Image Processing and Analysis, Data Sciences, Machine Learning, Statistical Analysis and Graph Theory. S/he should be proficient in programming in C++ and Python languages. Previous experience in modeling in the context of biology will be considered as an asset.

The position is opened for 3 years starting either in November or December 2019. Applicants must send by email a CV, a statement of interest, and 2 or 3 reference letters at christophe.godin@inria.fr(Mosaic project-team) and gregoire.malandain@inria.fr  (Morpheme project-team). Applications will be reviewed as received. So the interested applicants are encouraged to apply as soon as possible. For further information, candidate can contact christophe.godin@inria.fr with questions related to this position.

Location: Inria Mosaic team, UMR RDP, ENS de Lyon, France. http://www.ens-lyon.fr/RDP/?lang=en

Funding: Inria Project Lab Naviscope

Selected references of the host team related to this program

• Fernandez, R., Das, P., Mirabet, V., Moscardi, E., Traas, J., Verdeil, J.-L., G. Malandain and C. Godin. (2010). Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution. Nature Methods, 7(7), 547–553. http://doi.org/10.1038/nmeth.1472
• Guignard, L., Godin, C., Fiuza, U. M., Hufnagel, L., Lemaire, P., & Malandain, G. (2014). Spatio-temporal registration of embryo images. Biomedical Imaging (ISBI), 2014 IEEE 11th International Symposium on, 778–781. http://doi.org/10.1109/ISBI.2014.6867986
•  Cerutti, G., Ali, O., & Godin, C. (2017). DRACO-STEM: An Automatic Tool to Generate High-Quality 3D Meshes of Shoot Apical Meristem Tissue at Cell Resolution. Frontiers in Plant Science, 8, 13–15. http://doi.org/10.3389/fpls.2017.00353
•  Léo Guignard, Ulla-Maj Fiuza, Bruno Leggio, Emmanuel Faure, Julien Laussu, LarsHufnagel, Grégoire Malandain, Christophe Godin, Patrick Lemaire (2018). Contact-dependent cell-cell communications drive morphological invariance during ascidian embryogenesis bioRxiv 238741; doi: https://doi.org/10.1101/238741
• Leggio, B., Laussu, J., Carlier, A., Godin, C., Lemaire, P., & Faure, E. (2019). MorphoNet: an interactive online morphological browser to explore complex multi-scale data. Nature Communications, 1–8. http://doi.org/10.1038/s41467-019-10668-1