Project 11

Mechanogenetic modelling of embryogenesis driven by empirical evidence from 4D microscopy images

Supervisor: Dr.Matteo Cavaliere, co-supervisors: local: Dr. Liangxiu Han, Dr. Moi Hoon Yap, external: Dr. Z. Kriva (STUBA)

Research Objectives: Formulate a realistic multiscale, integrated mechanogenetic model of animal development, centred on the physico-chemical coupling of cell/tissue mechanics with gene expression and molecular signalling. Implement metaheuristic methods (e.g. genetic algorithms), to search parameter space and fit simulations to the imaging datasets.

Outreach Activities: Create an open-source software project (community of developers & end users) aimed for scalability and sustainability; and a “serious game” application (for exhibitions/live demos/workshops, and school visits for educational purposes).

Expected Results: A hybrid computational (agent-based) and mathematical/numerical (implicit-surface) modelling framework and simulation platform able to describe, reproduce, and ultimately explain, important developmental principles and episodes of the studied vertebrate embryos.

Outreach: 3D+time models immersed in a simulated physics environment and connected to a haptic peripheral device to create a micromanipulation training framework (“serious game”).


  • Academic: P3, CNRS N. Peyriéras, Training to the BioEmergences image processing workflow, and MecaGen modelling platform. P5 STUBA K. Mikula, Feature selection, segmentation, and implicit surface modelling.
  • Industrial: P10 Tatramed Softw, J. Urbán, Software implementation of the “serious game”.

Links to other projects: collaborations with ESR4,5,7&8 for Image processing and with ESR10&13 for modelling.