Missions

We are offering a post-doc position for 18 months (ANR funding) in the field of modelling and image processing for optical biomedical imaging. The work will take place at the Institut Fresnel in Marseille, within the DiMABio team, as part of a collaboration with the Optimal platform of the Institute for Advanced Biosciences (IAB) in Grenoble (https://iab.univ-grenoble-alpes.fr/Plateformes/imagerie-optique-petit-animal-optimal), and Kaer Labs in Nantes (https://www.kaerlabs.com/), for the development of a fluorescence tomography system in the second biological window NIR II (900-2000 nm). The candidate's mission will be to develop 3D reconstruction algorithms for the localisation of fluorescence sources detectable in vivo in mouse models.

Activities

Biomedical optical imaging is a fast-growing non-conventional imaging technique. Fluorescence Diffuse Optical Tomography (FDOT) is a non-invasive imaging technique capable of detecting and quantifying fluorescent sources located in deep organs in living organisms (rodents). The conventional FDOT technique uses non-ionising radiation in the visible to near infrared spectral range (600-900 nm, NIR I), in which biological tissues are relatively non absorbing but highly scattering. As part of this project, we want to explore the second therapeutic window, known as NIR II (from 900 nm to 2000 nm), where biological tissues are highly absorbing, mainly due to their high water content, but have lower scattering coefficients than in the visible range or NIR I, which gives us hope of images with better resolution, while accessing penetration depths compatible with the dimensions of small rodents (1 to 2 cm).
More specifically, the project concerns the development of a reconstruction algorithm using fluorescence images from a fluorescence imaging system for small animals in the "NIR-II" spectral range (1000 to 2000 nm). This algorithm must: i) be based on the numerical resolution of a light propagation model capable of taking into account the high levels of absorption and scattering of biological tissues at these wavelengths (Radiative Transfer Equation); ii) take into account the technical characteristics of the instruments (acquisition geometry, type of sensor and source, fluorescence filter, etc.). The candidate will be able to draw on preliminary work and numerical tools that have already been implemented (work started two years ago), as well as the expertise and infrastructure of the teams.

The algorithm developed will then be used to detect new organic (cyanine derivatives) and inorganic (gold nanoclusters) contrast agents with cancer-specific motif targeting functions. The in vivo biological behaviour of these contrast agents will be assessed after administration in mice. Initially, their in vivo biodistribution will be assessed in healthy mice, followed by an evaluation of their tumour-targeting capacity in mouse models of cancer.

The work will comprise the following 3 phases:
-Extension of numerical tools (resolution of direct and inverse problems) to exploit multi-dimensional signals (multi/hyperspectral imaging), and optimisation (co-design) of measurement chains (parameters linked to the instrumentation) and reconstruction chains (regularisation, choice of hyperparameters), using artificial intelligence tools to varying degrees. -Experimental validation on phantoms to demonstrate the benefits of the methods developed.
-Experimental validation on phantoms to demonstrate the benefits of the methods developed
-Exploitation of preclinical data (various types of contrast agents for targeting various organs/cancers) as part of studies conducted by IAB researchers.

Skills

- Holder of a PhD in applied mathematics, physics, computer science, image processing or a similar field.
- Skills in scientific computing (numerical analysis for PDEs, optimisation, algorithms, deep learning and HPC), signal and image processing.
- Knowledge of physical models would be a plus.
- Programming languages: Python, C/C++, MATLAB, CUDA (or openCL). - Knowledge of Linux OS and VTK library would be a plus
- Autonomous
- Team player
- Good level of English

Work Context

The work will be carried out at the Institut Fresnel in Marseille (https://www.fresnel.fr/wp/), as part of the DiMABio team, which focuses on the development of optical methods for biomedical diagnosis and imaging. The successful candidate will join a research project team of five permanent staff and one PhD student.

The position is located in a sector under the protection of scientific and technical potential (PPST), and therefore requires, in accordance with the regulations, that your arrival is authorized by the competent authority of the MESR.