Subject title: 3D advanced reconstruction algorithms reaching high spatial and temporal resolution for tomographic diffractive microscopy of biological living samples
Host laboratory: Laboratoire Hubert Curien (LaHC), 18 Rue Pr B. Lauras, 42000 SAINT-ÉTIENNE.
Supervisors: Fabien Momey (email@example.com), Corinne Fournier (firstname.lastname@example.org).
Keywords: Image processing, numerical modelization, image reconstruction, tomographic diffractive microscopy.
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. Tomographic diffractive microscopy (TDM) is a new technique, which permits to image transparent specimens in 3-D , without preparation or staining. It combines micro-holography with tomographic acquisitions, 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 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 HORUS project, 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 image processing for reconstruction. The goal is to adapt the technique to the imaging of living samples.
Subject of the Post-Doc:
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 [5,2,6]. The HORUS project particularely aims at exploring 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. In this context, one of the main concerns is the numerical modelization of the image formation process, which deals with 3D diffraction physics [12,13,14,6], and is a correlated task of the HORUS project.
The Hubert Curien Laboratory has a good expertise 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 (subject available on the web site of the GdR ISIS: http://www.gdr-isis.fr/news/5657/121/High-Resolution-Tomographic-Diffractive-Microscopy-Instrumentation-and-Image-processing.html), will also start soon, and will be highy interconnected with this Post-Doc.
Required skills: signal and image processing, physical optics (interferometry, diffraction). An experience in image reconstruction (digital holography, tomography) and/or inverse problems (modelization, regularization, numerical optimization) would be a valuable additional asset.
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(c) GdR 720 ISIS - CNRS - 2011-2020.