Subject title: Study, implementation and comparison of numerical models for simulating the image formation process in tomographic diffractive microscopy, to be applied in 3D reconstruction algorithms of biological living samples.
Host laboratory: Laboratoire Hubert Curien (LaHC), 18 Rue Pr B. Lauras, 42000 SAINT-ÉTIENNE.
Supervisors: Fabien Momey (firstname.lastname@example.org), Corinne Fournier (email@example.com).
Keywords: Image processing, numerical modelization, image reconstruction, tomographic diffractive microscopy.
Duration: 6 months.
Starting date: february/march 2019.
Salary: ~ 600 euros/month.
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 internship:
This internship is inserted in the improving task of 3D reconstruction algorithms. In this context, one of the main concerns is the numerical modelization of the image formation process, which deals with 3D diffraction physics.
The recruited candidate will have to make a review of existing models [5,6,7,8], to implement them in order to evaluate and compare their respective performances in terms of modelization accuracy, calculation time, and applicability to reconstruction algorithms. Matlab will be used for programming.
Interactions and transfers of knowledge will occur with the IRIMAS laboratory. This internship can continue with a PhD thesis mixing instrumentation and image processing in the context of the HORUS project (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).
 O. Haeberlé, K. Belkebir, H. Giovaninni, and A. Sentenac. Tomographic diffractive microscopy: basics, techniques and perspectives. Journal of Modern Optics, 57(9):686–699, May 2010.
 Matthieu Debailleul, Bertrand Simon, Vincent Georges, Olivier Haeberlé, and Vincent Lauer. Holographic microscopy and diffractive microtomography of transparent samples. Measurement Science and Technology, 19(7):074009, 2008.
 B. Simon, M. Debailleul, V. Georges, V. Lauer, and O. Haeberlé. Tomographic diffractive microscopy of transparent samples. The European Physical Journal - Applied Physics, 44(1):29–35, October 2008.
 Bertrand Simon, Matthieu Debailleul, Mounir Houkal, Carole Ecoffet, Jonathan Bailleul, Joël Lambert, Arnaud Spangenberg, Hui Liu, Olivier Soppera, and Olivier Haeberlé. Tomographic diffractive microscopy with isotropic resolution. Optica, 4(4):460–463, April 2017.
 U. S. Kamilov, I. N. Papadopoulos, M. H. Shoreh, A. Goy, C. Vonesch, M. Unser, and D. Psaltis. Optical Tomographic Image Reconstruction Based on Beam Propagation and Sparse Regularization. IEEE Transactions on Computational Imaging, 2(1):59–70, March 2016.
 Emmanuel Soubies, Thanh-An Pham, and Michael Unser. Efficient inversion of multiple-scattering model for optical diffraction tomography. Optics Express, 25(18):21786–21800, September 2017.
 H. Y. Liu, D. Liu, H. Mansour, P. T. Boufounos, L. Waller, and U. S. Kamilov. SEAGLE: Sparsity-Driven Image Reconstruction under Multiple Scattering. IEEE Transactions on Computational Imaging, PP(99):1–1, 2017.
 J. Bailleul, B. Simon, M. Debailleul, L. Foucault, N. Verrier, and O. Haeberlé. Tomographic diffractive microscopy: Towards high-resolution 3-D real-time data acquisition, image reconstruction and display of unlabeled samples. Optics Communications, 422:28–37, September 2018.