PhD position Development and validation of accelerated multi-scale simulation codes for X-ray emission tomography imaging (M/F)

Job Description

Thesis Subject

The objective of this PhD project is to simulate X-ray fluorescence emission imaging experiments, particularly for applications in biology, from the cellular scale to small-animal imaging. This imaging technique is quantitative, providing access to chemical composition with high sensitivity. This information is crucial, as the distribution of inorganic chemical elements serves as a marker of many biological mechanisms that can thus be revealed. Depending on the scale studied (cell, organ, small animal), different radiation sources (protons, X-rays) with appropriate energies are used. However, obtaining accurate quantitative images remains a major challenge due to the complexity of the physical phenomena and reconstruction processes. The PhD candidate will be responsible for developing a digital twin (in the broad sense) dedicated to the simulation of these experiments. The ultimate goal is to optimize experimental setups and tomographic image reconstruction methods while minimizing acquisition time and deposited dose.

Your Work Environment

The PhD candidate will work in an interdisciplinary research environment at the interface of Physics, Biology, and Computer Science. Supervision will be provided by Claire Michelet, physicist, Professor at LP2IB, Pascal Desbarats, computer scientist, Professor at LaBRI, Jean Michel Létang, Associate Professor at CREATIS (Lyon). PhD progress will be monitored through weekly meetings to ensure effective guidance.
Complementary Information
National collaborations:
The PhD project is based on a partnership between three laboratories:
- Laboratory of Physics of the Two Infinities Bordeaux (LP2IB): a pioneer in X-ray emission micro-imaging, particularly on C. elegans, with a dedicated proton microbeam line and long-standing expertise in simulation of spectra and X-ray emission tomography images.
- Computer Science Research Laboratory of Bordeaux (LaBRI): develops original deterministic simulation methods, notably based on the gVXR library, enabling rapid generation of large amounts of synthetic data. The digital twin developed during the PhD will provide a “gold standard” to validate the reliability of these datasets. These synthetic data are particularly valuable for developing new image reconstruction methods based on deep learning, especially in sparse or incomplete acquisition scenarios, where experimental data are insufficient.
- Center for Research in Acquisition and Processing of Signals for Health (CREATIS): a multidisciplinary medical imaging laboratory playing a major role in health technologies. One objective is to develop new algorithms for Monte Carlo simulations (Geant4/GATE), including variance reduction techniques, as well as innovative reconstruction methods for imaging systems.

International collaborations:
- The Australian Synchrotron and the Florey Institute of Neuroscience and Mental Health: bring expertise in X-ray emission micro-imaging using synchrotron radiation. Experiments aiming to establish a 3D map of the metallome of C. elegans are currently conducted in collaboration with LP2IB.
- Daresbury Laboratory Imaging Group (Scientific Computing, STFC): develops deterministic simulation methods, particularly the gVXR library, for rapid generation of large synthetic datasets used for training deep learning algorithms. One objective of the digital twin developed in this PhD will be to provide a “gold standard” to validate these methods by identifying systematic biases (e.g., self-absorption or line broadening), thereby guiding calibration of simplified physical models and variance reduction schemes in gVXR.

Compensation and benefits

Compensation

2300 € gross monthly

Annual leave and RTT

44 jours

Remote Working practice and compensation

Pratique et indemnisation du TT

Transport

Prise en charge à 75% du coût et forfait mobilité durable jusqu’à 300€

About the offer

About the CNRS

The CNRS is a major player in fundamental research on a global scale. The CNRS is the only French organization active in all scientific fields. Its unique position as a multi-specialist allows it to bring together different disciplines to address the most important challenges of the contemporary world, in connection with the actors of change.

CNRS

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