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Study or research engineer for phase image processing

ABG-101292 Emploi Junior
19/11/2021 CDD 14 Mois > 25 et < 35 K€ brut annuel
LIEC-UMR CNRS-Université de Lorraine
Nancy - Grand Est - France
Sciences de l’ingénieur
  • Ecologie, environnement
  • Physique
label free imaging; photonics; image simulation; data processing
19/01/2022
Enseignement et recherche

Employeur

The LIEC (Interdisciplinary Laboratory of Continental Environments) is an interdisciplinary laboratory of University of Lorraine and CNRS. The research carried out there aims to understand the functioning of continental ecosystems strongly disturbed by human activity, with the aim of their rehabilitation. To this end, we carry out interdisciplinary research combining concepts and methods coming from environmental mineralogy, soil science, microbial ecology, colloidal physico-chemistry, ecotoxicology, functional ecology.

To map and evaluate the properties of nano/micrometric-sized environmental objects such as nanoparticles, mineral phases or microorganisms such as bacteria and algae, the laboratory is equipped with a set of advanced optical microscopy instruments, including systems dedicated to label free imaging (3D-holotomography and 2D-phase camera).

Poste et missions

You will participate in the development of new strategies for the processing of phase images recorded by holotomography or with a phase camera.

Your mission will be to generate or simulate 3D optical index distributions (for example, creation of Shepp-Logan like phantoms modified to be relevant to mimic microorganisms). From these volumes, 2D projections will be deduced (Radon transformation) and the equivalent of small angles scattering curves will be calculated by Fourier transform.

The objective is to compare the curves calculated from synthetic phantoms to the one derived from measurements on real biological objects (bacteria, microalgae, etc.) to understand their particular characteristics. Depending on the progress of the project, the implementation of deep learning approaches for curves classification is envisaged.

You will also participate in the acquisition of images on biological samples and contribute to the development of experimental strategies, including comparing the results obtained from 2D holotomography and phase microscopy instruments.

Mobilité géographique :

Pas de déplacement

Prise de fonction :

14/02/2022

Profil

You have a master's degree, an engineering degree or a PhD specialized in one of the following fields: optics, photonics, physics, computer science, applied mathematics or image processing - data science.

You are familiar with Matlab or Python programming to model and process data. You have an interest in the programming required for image processing and in imaging experiments.

You are autonomous and rigorous. You enjoy working in a team, in an interdisciplinary context (from physics to environmental biology). You are able to report regularly on the results obtained. Fluency in English is essential.

Objectifs

The project will run over a period of 14 to 18 months, depending on your degree level (14 months for doctor or engineer/ 18 months for master).

At the end of the project, you will have built a database of synthetic images (or ghosts) from which you will have generated scattering curves. All the calculated curves will be compared with ones recorded on real objects to identify the curves characteristics that are linked to the objects biophysical properties. Results will be published in scientific articles.

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