PhD Position: OrganoDyn: Organoid dynamic reconstruction across scales: how do cell motions build tissue shapes?

OrganoDyn: Organoid dynamic reconstruction across scales: how do cell motions build tissue shapes ?

Keywords
Organoid, development, cell tracking, multiscale motion analysis, live-microscopy data.


The first steps of mammalian development can be reproduced from a completely homogeneous assemblies of stem cells. The understanding of such complex 3D processes requires new computer vision approaches for the automated exploration of 3D microscopy imaging.

Supervision
Dr. Philippe Roudot (CENTURI and Institut des Mathématiques de Marseille)
Dr. Sham Tlili (Institut de biologie du développement de Marseille)
Pr. Pierre-François Lenne (Institut de biologie du développement de Marseille)

Abstract
Embryonic organoids are in vitro multi-cellular aggregates that self-organize and reproduce the hallmarks of morphogenesis. Within this class of in vitro systems, gastruloids recapitulate the first steps of mammalian development. Understanding how symmetry breaking arises spontaneously from homogeneous cell assemblies requires the interrogations of the functional link between temporal variations in single cell signaling, cellular cluster behavior, and organoid shape. While computer vision tools have been designed to measure the changes in cellular flow and general shape in such systems, the tracking of individual cells nested in those thick samples remains challenged by density, variable signal-to-noise ratio, limited acquisition framerate and the heterogeneous nature of motions. The PhD candidate will thus develop new approaches for the reconstruction of motions contribution, from single cell to multicellular flows. Inspired by our previous work on multiple particle tracking, we will investigate a graph-based approach for the tracking of individual cells using multiscale motion modeling, genetic expression modeling and model selection approaches. The student will also have the opportunity to use those tools to investigate how local signaling clusters may drive morphogenesis, and in turn, how the variations in system shapes may influence those local events.

Expected profile
The PhD student will have a formal training in applied mathematics or computer science with a keen interest in biophysics, cell biology and study of complex systems.

More info PHD2021-21 | OrganoDyn - Centuri Living Systems
How to apply Application Form - PhD2021-21 - Centuri Living Systems
Application Deadline February 26 2021