title: An integrated modelling framework from cells to organism based on a cohort of digital embryos.
abstract: We conducted a quantitative comparison of developing sea urchin embryos based on the analysis of five digital specimens obtained by automatic processing of in toto 3D+ time image data. These measurements served the reconstruction of a prototypical cell lineage tree able to predict the spatiotemporal cellular organisation of a normal sea urchin blastula. The reconstruction was achieved by designing and tuning a multi-level probabilistic model that reproduced embryo-level dynamics from a small number of statistical parameters characterising cell proliferation, cell surface area and cell volume evolution along the cell lineage. Our resulting artificial prototype was embedded in 3D space by biomechanical agent-based modelling and simulation, which allowed a systematic exploration and optimisation of free parameters to fit the experimental data and test biological hypotheses. The spherical monolayered blastula and the spatial arrangement of its different cell types appeared tightly constrained by cell stiffness, cell-adhesion parameters and blastocoel turgor pressure.
authors.affiliation: BioEmergences Laboratory USR3695, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.|Complex Systems Institute Paris Île-de-France (ISC-PIF) UPS3611, CNRS, 113 rue Nationale, 75013 Paris, France.
authors.forename: Paul
authors.initials: P
authors.lastname: Villoutreix
authors.affiliation: BioEmergences Laboratory USR3695, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.|Complex Systems Institute Paris Île-de-France (ISC-PIF) UPS3611, CNRS, 113 rue Nationale, 75013 Paris, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Delile
authors.affiliation: BioEmergences Laboratory USR3695, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.|Complex Systems Institute Paris Île-de-France (ISC-PIF) UPS3611, CNRS, 113 rue Nationale, 75013 Paris, France.
authors.forename: Barbara
authors.initials: B
authors.lastname: Rizzi
authors.affiliation: BioEmergences Laboratory USR3695, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.|Complex Systems Institute Paris Île-de-France (ISC-PIF) UPS3611, CNRS, 113 rue Nationale, 75013 Paris, France.
authors.forename: Louise
authors.initials: L
authors.lastname: Duloquin
authors.affiliation: BioEmergences Laboratory USR3695, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.|Complex Systems Institute Paris Île-de-France (ISC-PIF) UPS3611, CNRS, 113 rue Nationale, 75013 Paris, France.
authors.forename: Thierry
authors.initials: T
authors.lastname: Savy
authors.affiliation: BioEmergences Laboratory USR3695, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.|Complex Systems Institute Paris Île-de-France (ISC-PIF) UPS3611, CNRS, 113 rue Nationale, 75013 Paris, France.
authors.forename: Paul
authors.initials: P
authors.lastname: Bourgine
authors.affiliation: BioEmergences Laboratory USR3695, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.|Complex Systems Institute Paris Île-de-France (ISC-PIF) UPS3611, CNRS, 113 rue Nationale, 75013 Paris, France.
authors.forename: René
authors.initials: R
authors.lastname: Doursat
authors.affiliation: BioEmergences Laboratory USR3695, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.|Complex Systems Institute Paris Île-de-France (ISC-PIF) UPS3611, CNRS, 113 rue Nationale, 75013 Paris, France.
authors.forename: Nadine
authors.initials: N
authors.lastname: Peyriéras
mesh_terms: D000818:Animals; D001696:Biomechanical Phenomena; D036703:Blastula / Q000166:cytology* / Q000502:physiology; D019070:Cell Lineage / Q000502:physiology*; D049109:Cell Proliferation; D048429:Cell Size; D003198:Computer Simulation; D007091:Image Processing, Computer-Assisted / Q000706:statistics & numerical data*; D021621:Imaging, Three-Dimensional; D015233:Models, Statistical; D012617:Sea Urchins / Q000166:cytology / Q000196:embryology* / Q000502:physiology