PhD Bioimage Mining lab

PhD Bioimage Mining lab

Multiscale stochastic filtering for dynamic processes in fluorescence microscopy

Host laboratory and collaborators

Philippe Roudot / I2M /


A fundamental challenge in the analysis of molecular dynamics stems from the low framerate imposed by fluorophores limitations. Conventional solutions include the modeling of a few representative motion types embedded in temporally greedy estimator. However, those efficient strategies are limited to sparse and homogeneous scenarios. This is especially problematic in 3D environments where cells and tissues move with a high degree of freedom. Accurately describing object displacements requires taking into account their multiscale nature: from diffusive behavior to rapid changes in cellular morphology and environmental forces.
Building upon our previous work, this research project will focus on the development of a piecewise-stationary model in space and time for the shared dynamic footprint of molecules. Model selection and boundaries detection will be approached through the use of stochastic filtering as well as their approximation
with deep neural networks. Expected challenges include the investigation of scalable approaches for assignment of model prediction to measurement as well as the definition or training of a handful of priors applicable to a wide variety of scenarios.
In addition to enable the quantification of dynamics that is not currently within reach, we aim at providing a generic framework for the analysis of collective motions across scales. Those approaches will be calibrated in collaborative studies ranging from intracellular transport to multi-cellular flow in embryonic model.


The training will focus on computer vision approaches for fluorescence microscopy with a strong emphasis on dynamic modeling, filtering and discrete optimization.
Support will also be provided toward efficient scientific communication with interlocutor of very diverse expertises.

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 the study of complex systems.


CENTURI offers a three-year contract from the University of Aix-Marseille. The salary will be based on Aix-Marseille University’s salary scale, depending on the candidate’s profile and experience.

If you are interested, we encourage you to apply by sending your application to Philippe Roudot (

Applications must include:

  • A CV
  • A cover letter
  • Two references we can contact

Deadline : until the position is filled