Computational modelling of biological dynamics using 3D computer vision: application to microbial decomposition in soil

Information technology is becoming more and more a key tool to address global life sciences challenges. Within this context, computational biology is a growing area mainly due to the today crucial ecological questions such as for instance carbon sequestration. This talk deals with the simulation of microbial decomposition in soil at microscopic scale using advanced computer vision algorithms to represent 3D soil microstructures. In particular, this issue faces the still open problem of the intrinsic and compact representation of 3D complex natural geometrical structures. Our simulation tools based on graph and Partial Differential Equations are validated using real experimental data.

This work belongs to the very first ones aiming at simulating, using real data, microbial decomposition in soil at micro scale (1-5 micron m) by taking into account 3D pore space representation. Such cross roads research can be very valuable for soil science in order to understand better soil microstructure impact on biological dynamics and also to evaluate biological scenarios difficult to implement experimentally. Same as for macroscopic physics versus quantic physics the final challenge is to understand relationships between biological phenomena at microscopic scale and at macroscopic scale. This refers to emerging properties, which is a fundamental issue in life sciences. Our methodology applies for any modelling problem where transformation, transport and diffusion processes occur simultaneously within complex 3D geometrical shapes. Therefore, it can be easily adapted for many other environment and medical applications.


Olivier MONGA is research director at IRD (France) formerly at INRIA (France).His research field is computer vision and its applications to complex system modeling. He gets his PhD degree in 1988 under the supervision of Pr. Olivier Faugeras and his habilitation to conduct researches in 1993 under the supervision of Pr. Nicholas Ayache, at the university Paris 11 (Orsay). He published over 100 papers in international journals and conferences and wrote a reference book ( He was the founding director of sino-french laboratory LIAMA and the initiator and manager of European pilot projects ANFAS and SIMES. Recently, he brought a major contribution to ANR project MEPSOM (2009-2013, who was selected as key project by ANR SYSCO program (Complex system mathematical modeling).