Subject title: 3D reconstruction algorithms for Optical Diffraction Tomography of biological living samples.
Host laboratory: Laboratoire Hubert Curien (LaHC), 18 Rue Pr B. Lauras, 42000 SAINT-ÉTIENNE.
Supervisor: Fabien Momey (firstname.lastname@example.org).
Keywords: Image processing, inverse problems, image reconstruction, deep learning, numerical modelization, optical diffraction tomography.
Duration: 20 months.
Starting date: as soon as possible.
Salary: ~ 2200 euros/month net (for experience post-PhD <= 3 years).
Context and problematics:
Optical microscopy techniques are among the preferred methods for biological studies, thanks to their unique capability of imaging living specimens in 3-D. Optical diffraction tomography (ODT) or Tomographic Diffractive Microscopy (TDM) is an emergent technique, which permits to image transparent specimens in 3-D , without preparation or staining. It uses digital holography microscopy acquisitions in "tomographic" mode, performed by either specimen rotation or illumination scanning. It allows for the measurement of the specimen index of refraction distribution in 3-D, and with a resolution twice better than conventional microscopy.
IRIMAS (Mulhouse) has built such a microscope [2,3], which has demonstrated its ability to reach an isotropic 3-D resolution in the 100 nm range . The state-of-art 3D reconstruction principle consists in a 3D mapping of the object of interest's frequencies space, as in conventional X-ray tomography (Fourier slice theorem). The more an isotropic coverage of the angular hologram acquisitions, the more the 3D frequency spectrum of the object can be fulfilled.
The ANR HORUS project [https://anr.fr/Projet-ANR-18-CE45-0010], involving a collaboration between the IRIMAS laboratory (Mulhouse), the Hubert Curien laboratory (Saint-Étienne) and the IGBMC institute (Strasbourg), and funded by the Agence Nationale de la Recherche (ANR), aims at improving this imaging technique in terms of instrumentation and reconstruction algorithms. The goal is to adapt the technique to the imaging of living samples. The goal of IGBMC team is to benefit from a complementary imaging technique - combined with fluorescence microscopy - to study the mechanisms of the HIV virus infection process. The expertise in optical instrumentation is carried out by IRIMAS, while The Hubert Curien laboratory brings its expertise in inverse problems dedicated to image reconstruction in microscopy and tomography.
Subject of the Post-Doc : 3D reconstruction algorithms
The Post-Doc is inserted in the improving task of 3D reconstruction algorithms, which is an active research area. The recruited candidate will have to improve or overcome already existing reconstruction methods, mostly based on the direct inversion of first Born approximation (the above mentioned 3D frequency spectrum mapping algorithm) [2,5,6].
The HORUS project particularely aims at exploring regularized inverse problems approaches to perform the reconstruction [7,8,9,10,11], with the ambitious challenge of reaching high spatial and temporal resolution to make possible to image microscopic living samples. Jointly exploring deep learning based methods for the reconstruction task  can also be an interesting field of research following the recruited candidate skills. In this context, another concern is the numerical modelization of the image formation process, which deals with 3D diffraction physics [6,13,14,15], and is a correlated task of the HORUS project.
The Hubert Curien Laboratory team is specialized in image reconstruction based on inverse problems strategies, applied to digital holographic microscopy . Already existing tools and algorithms (models, optimization methods, regularizations) will be available to the candidate, that have been implemented and used in the team for image reconstruction of hologram data.
High interactions and transfers of knowledge will occur with the IRIMAS laboratory. A PhD thesis at IRIMAS, mixing instrumentation and image processing, will also start soon, and will be highy interconnected with this Post-Doc.
Required skills: signal and image processing, 2D/3D image reconstruction (digital holography, tomography) and/or inverse problems (modelization, regularization, numerical optimization). A background in deep learning approaches applied to image reconstruction could be also of interest to be combined to the targeted regularized inversion methods.
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(c) GdR 720 ISIS - CNRS - 2011-2020.