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PhD Proposal:HYPERSPECTRAL TOMOGRAPHIC DIFFRACTIVE MICROSCOPY: RESEARCH AND APPLICATIONS

30 Juillet 2024

Catégorie : Doctorant

The IMTIS team at IRIMAS (Mulhouse) has developed a recognized experience in instrumentation and image processing for microscopy (In 2023, HCERES (French evaluation agency for research and higher education) has highlighted our “instrumentation in microscopy” research domain among the “outstanding scientific results” of Université de Haute-Alsace, benefitting from international recognition.

To pursue this work, we propose a PhD entitled "Hyperspectral Tomographic Diffractive Microscopy", an extension of our previous development, aiming at restoring chemical sensitivity in tomographic microscopy.

We are therefore seeking for talented students, interested in both instrumentation and associated data/image processing, to join our dynamic team, working in collaboration with another PhD student working on another variant of this approach.

Phd Advisors (contact both, please):

Dr HDR Nicolas Verrier nicolas.verrier@uha.fr +33 3 89 33 76 66

Pr Olivier Haeberlé olivier.haeberle@uha.fr +33 3 89 33 76 61

PhD Proposal :

Quantitative phase imaging (QPI) becomes more and more popular in biomedical imaging, especially in optical microscopy. Unlike other methods relying on fluorescence of contrast agents, incorporated into the sample, QPI extracts phase and amplitude directly from the optical field transmitted or reflected by the object, rendering sample labeling optional.

Within the IMTIS (Multimodal Imaging, Information and Signal Processing) team at IRIMAS (Institut de Recherche en Informatique, Mathématiques, Automatique et Signal), we have been developing, for about 15 years now, a generalization of QPI called Tomographic Diffractive Microscopy (TDM) [1-4]. By varying the object's illumination conditions, it is possible to obtain a 3D reconstruction of its complex refractive index (in absorption and refraction), with improved resolution compared to conventionnal QPI approaches [1,5,6].

These methods offer an interesting alternative to flurorescence microscopy, but suffer from a lack of chemical selectivity in the reconstructed information. Indeed, very different structures may have a similar refractive index. The aim of this innovative PhD proposal is to develop new approaches, in order to restore selectivity to tomographic images.

Preliminary studies have shown that it is indeed possible to access quantitative polarization information, offering structural selectivity by distinguishing non-birefringent and birefringent elements [7,8]. Dynamic selectivity is also possible: heterodyning of the detected signal allow for isolating moving structures within a sample by measuring the Doppler effect induced on scattered light [9].

Another possible approach is based on multispectral or hyperspectral imaging (spectro-imaging), which is the topic of this PhD proposal. In particular, it has already been proven that the variation of absorption with wavelength enables chemical species to be distinguished at the micrometric scale. [10,11].

The proposed PhD is therefore twofold: an experimental aspect, to, among others, upgrade the instrument with a white-light laser in order to acquire the necessary data [5,6], and a numerical aspect, to improve tomographic image reconstruction algorithms using these new data [12].

For such a project, both a taste for experimental work (optics, microscopy), as well as a sound knowledge of imaging and signal processing is mandatory. The successful candidate will be proficient in an object-oriented programming language (C++, Python, Matlab, etc.).

You will be part of a dynamic team with recognized scientific expertise, and benefit from its already available equipment and operating resources (to attend conferences, pay publication fees, etc.). Standard PhD fellowhip : 2100 €/month (2024) to 2300 €/month (2026).