Institut Fresnel

Post-doctoral position for the development of nonlinear microscopy in the field of cancer diagnostics

Funding : ERC Consolidators grant

Duration : 36-month – Starting date September 2024

Salary : ≥ 2400€ negotiable

Supervisor : Dr. Sandro Heuke, Chargé de Recherche at the CNRS

Research team : MOSAIC

Address : Institut Fresnel, Av Escadrille Normandie-Niémen, 13397 Marseille Cedex 20, France.

Our mission
Our rent advances in coherent Raman microscopy allow for the real-time generation of artificially stained images of cancer samples which previously required time-consuming histopathological staining procedures. These images serve as feedback for surgeons to guide cancer surgery. As the main challenge, the examination of thick cancer samples is currently impossible, as all excitation light in coherent Raman microscopy is scattered forward and must pass through the sample. Within this project, you will develop a new coherent Raman technique called coherent Stokes Raman scattering (CSRS) microscopy. As the game-changer, CSRS will send the signal photons directly into the backward direction and, therefore, enable the investigation of thick, non-transparent cancer samples. Moreover, we will use CSRS’ backscattering property to record the CSRS spectrum of tissue at unprecedented speed levels using novel spectrometer concepts and multi-focus or wide-field illumination approaches. From these CSRS spectra, a precise diagnosis of the cancerous tissue will be derived by machine learning algorithm. Your mission is to set up and characterize these novel microscopy techniques and evaluate their functionality on cancer tissue.

Your Profile

Attitude : For you, research is a vocation and not just a source of income. High levels of initiative, creativity and curiosity are expected from you.

Willingness to perform : During university education you were always in the top 20% and you should have at least 2 major publications as first author.

Qualification : You have completed a degree in the field of photonics, e.g. physics, physical chemistry or similar. You have developed microscopy techniques or other imaging methods during your doctorate.

Curious ? Please send a letter of motivation, a detailed CV, a reference letter and 3 academic references to Sandro.Heuke@fresnel.fr.

New algorithmic approaches for Fluorescence Diffuse Optical Tomography in the second biological window

Researcher offer : New algorithmic approaches for Fluorescence Diffuse Optical Tomography in the second biological window (SWIR)

Principal Investigator : Dr Anabela Da Silva, PhD, Senior researcher at CNRS - Email : anabela.dasilva@fresnel.fr

Research team : DiMABio, Institut Fresnel / CERIMED

Address : Institut Fresnel, Av Escadrille Normandie-Niémen, 13397 Marseille Cedex 20, France. Work carried out in partnership with KAER LABS (Nantes) and Institut pour l’Avancée des Biosciences (IAB, Grenoble)

Funding : Fondation AMIDEX, 12 months

We are offering a 12-month post-doc position (AMIDEX funding) in the field of modeling and image processing for optical biomedical imaging. The work will take place at the Institut Fresnel in Marseille, within the DiMABio team, as part of a collaboration with the Optimal platform of the Institut pour l’Avancée des Biosciences (IAB) in Grenoble, and Kaer Labs in Nantes, for the development of a fluorescence tomography system in the second biological window NIR II or SWIR (Short Wave InfraRed 900-1700 nm). The candidate’s mission will be to develop 3D reconstruction algorithms for the localization of fluorescence sources detectable in vivo in mouse models.

Scientific background and objective :
Optical biomedical imaging is a fast-growing non-conventional imaging technique. Fluorescence Diffuse Optical Tomography (FDOT) is a non-invasive imaging technique capable of detecting and quantifying localized fluorescent sources in deep organs of living organisms (rodents). Conventional FDOT uses non ionizing radiation in the visible to near infrared spectral range (<900 nm, NIR I), in which biological tissues are relatively unabsorbent but highly scattering. As part of this project, we intend to explore the second therapeutic window, known as NIR II or SWIR (shortwave infrared) (900 nm to 1700 nm), where biological tissues are highly absorbent, mainly due to their high water content, but have lower scattering coefficients than in the visible range or NIR I, giving rise to the hope of higher resolution images, while accessing penetration depths compatible with the dimensions of small rodents (1 to 2 cm). More specifically, the project concerns the development of a reconstruction algorithm using fluorescence images from a small animal fluorescence imaging system similar to that described in publications [1-4], but in the "NIR-II" or "SWIR" spectral range (1000 to 1700 nm), co-developed by Kaer Labs, IAB and Institut Fresnel. This algorithm must : i) be based on the numerical resolution of a light
propagation model capable of taking into account the high absorption and scattering levels of biological tissues at these wavelengths (Radiative Transfer Equation) ; ii) take into account the technical characteristics of the instruments (acquisition geometry, type of sensor and source, fluorescence filter, etc.). The candidate will be able to draw on preliminary work and numerical tools already implemented (work started two years ago), as well as on the expertise and infrastructures of the teams.

The algorithm developed will then be applied to the detection of new organic (cyanine derivatives) and inorganic (gold nanoclusters) SWIR contrast agents [5] with cancer-specific motif targeting functions. The in vivo biological behavior of these contrast agents will be evaluated after administration in mice. First, their in vivo biodistribution will be assessed in healthy mice, then their tumor-targeting capacity will be evaluated in mouse models of cancer [6].

The work will thus comprise the following 3 phases :
 Implementation of numerical tools, in particular the development of a Radiation Transfer Equation solver using Monte Carlo simulations or the Finite Element Method, optimized for coupling to a reconstruction algorithm.
 Experimental validation on phantoms
 Pre-clinical study

Key words : Inverse problems, Diffuse Optical Tomography (DOT), Radiative Transfer Equation, Small Animal Imaging, Fluorescence in NIR I (Near InfraRed 600-900 nm), NIR II or SWIR (Short Wave InfraRed 900-1700 nm)

Candidate profile :
As the models and methods for solving the equations are known, this project requires strong skills in numerical modeling (solving the Radiation Transfer Equation using numerical or stochastic methods), applied mathematics and information processing. The multi-disciplinary context, at the interface between physics and biomedical research, calls for an independent and open-minded candidate, capable of taking experimental and biological constraints into account. The main skills required for the project concern knowledge of physical models, scientific computing (numerical analysis for PDEs, optimization, algorithms, Deep Learning and HPC), signal and image processing. No specific chemistry or biology skills are required, but candidates should be open to the prospect of contributing to these experiments.

Programming languages : C/C++, Python, MATLAB, VTK, CUDA.

Candidates are requested to submit :
 a cover letter explaining shortly the relevance and motivation of the application
 a detailed CV
 2 major publications
 2 academic references

The application should be addressed to anabela.dasilva@fresnel.fr

New algorithmic approaches for Fluorescence Diffuse Optical Tomography in the second biological window (SWIR)

Description : Nous proposons une offre de poste de chercheur/chercheuse (post-doc) sur une durée de 12 mois
(financement AMIDEX) dans le domaine de la modélisation et du traitement d’image pour l’imagerie biomédicale optique. Les travaux se dérouleront à l’Institut Fresnel à Marseille, au sein de l’équipe DiMABio https://www.fresnel.fr/spip/spip.ph...,, dans le cadre d’une collaboration avec la plateforme Optimal de l’Institut pour l’Avancée des Biosciences (IAB) à Grenoble https://iab.univ-grenoble-alpes.fr/..., et la société Kaer Labs à Nantes https://www.kaerlabs.com/, pour le développement d’un système de tomographie de fluorescence dans la seconde fenêtre biologique NIR II ou SWIR (Short Wave InfraRed 900-1700 nm). La mission du candidat
sera de développer des algorithmes de reconstruction 3D

Laboratoire : Institut Fresnel, Marseille

Responsable : Da Silva Anabela, équipe DIMABIO

Financement : AMIDEX

Durée : 12 mois

Contact : Anabela Da Silva anabela.dasilva@fresnel.fr

Postdoc Smart microscopes & their application to imaging of biological tissues

Postdoctoral position position to study smart microscopes and their application to imaging of biological tissues

Description : We are looking for an enthusiastic, ambitious candidate to join our efforts in elucidating animal septin organization and function. Applicants should have a Master’s or PhD degree in applied physics, biophysics, data science, or a related field, experience in the development of optical instruments, particularly in the field of optical microscopy, and proficiency in programming (MATLAB, Python) and image processing.

Laboratoire : Institut Fresnel, Marseille
Direction de thèse : Loïc Le Goff, équipe MOSAIC
Financement : ANR
Contact : loic.legoff@fresnel.fr
Interested applicants are invited to submit a letter of interest, a CV, and contact information for 2 references

Recrutement ATER CNU 63

Enseignant en Métrologie, Chaines de Mesures, Capteurs, Electromagnétisme et Optique / Recherche expérimentale en Imagerie, Nanophotonique, Composants optiques ou Electromagnétisme

Section CNU : 63
Date Prise de fonction : 01/09/2023
Durée min. : 12 mois à 100%

Enseignement au Département de Mesures Physiques
Le(a) candidat(e) retenu(e) sur ce poste sera appelé(e) à effectuer des Travaux Dirigés et des Travaux Pratiques de Métrologie, Chaines de Mesures, Capteurs, Électromagnétisme et Optique au sein du département Mesures Physiques de l’IUT de Marseille.
Contact : Mme Stéphanie Escoubas, Directrice du département - stephanie.escoubas@univ-amu.fr

Recherche à l’Institut Fresnel - UMR7249.
Le(a) candidat(e) rejoindra l’une des équipes du laboratoire et travaillera dans l’un des domaines suivants : imagerie optique, nanophotonique, composants optiques, électromagnétisme. Le candidat devra impérativement avoir une expérience en physique expérimentale dans l’un de ces domaines.
Contact : Mme Sophie Brasselet, Directrice d’unité - sophie.brasselet@fresnel.fr

 Research Field EURAXESS : http://ec.europa.eu/euraxess/index.cfm/jobs/jobsByResearchField

Postdoctoral position to study the role of septins in epithelial tissues

Description : We are looking for an enthusiastic, ambitious candidate to join our efforts in elucidating animal septin organization and function. Applicants should have a background in cell or developmental biology, bioengineering, biophysics, or a closely related field. Prior experience with Drosophila genetics and handling, tissue mechanics measurements, or image analysis and data science will be a plus, but is not required.

Laboratoire : Institut Fresnel, Marseille

Direction de thèse : Loïc Le Goff et Manos Mavrakis

Financement : ANR

Durée : 36 mois - Starting date as early as spring 2023

Contact : Interested applicants are invited to submit a letter of interest, a CV, and contact information for two references to Loïc Le Goff (loic.legoff@fresnel.fr) and Manos Mavrakis (manos.mavrakis@fresnel.fr)

Postdoc Position SEPTISS

Post-doctoral...

Description : The selected post-doctoral researcher will take active part in the ERC project, which requires :
 Design and implementation of an in-situ mechanical test rig, with support from a research engineer
 Experimental characterization of the bone-tendon insertion with texture tomography during in-situ mechanical deformation at synchrotron light sources (e.g. European Synchrotron (ESRF), Grenoble, France)

The selected post-doc should demonstrate a sound scientific background and very good knowledge of experimental methods, allowing him/her to conduct the outlined research activities. He/she will work under the direct supervision of a CNRS scientist and will interact with other researchers in the team, scientific collaborators in biomechanics as well as scientists at the ESRF during the implementation of the method. The position entails furthermore multiple scientific visits to the European Synchrotron (ESRF) during the implementation of the in-situ experiment. The working language in the team is English.

Laboratoire : Institut Fresnel, Marseille

Partenariat : ERC starting grant

Durée : 24 month postdoctoral position starting preferentially in Fall of 2023

Contact : Tilman Grunewald - tilman.grunewald@fresnel.fr

Postdoc TexTOM

Post-doc Mathématiques Appliqués

Le projet concerne l’étude de la propagation dans des guides d’ondes de géométrie spécifique obtenus par une torsion (non nécessairement constante) d’un guide droit de section quelconque le long de son axe longitudinal.

Lieu : Institut Fresnel, Marseille. Ce projet regroupe 3 chercheurs en mathématiques appliquées et en physique mathématique du Centre de Physique Théorique (CPT), de l’Institut Fresnel et de l’Institut de Mathématiques de Marseille (I2M).

Durée : 24 mois - Début souhaité entre avril et septembre 2023
Pré-requis : Doctorat avec bagage important sur les équations aux dérivées partielles, en théorie spectrale et une bonne formation en physique théorique (physique quantique, acoustique, électromagnétisme) et en informatique scientifique.
Candidature : Envoyer un email à Maxence CASSIER avant le 15 février 2023 avec un CV détaillé comportant la liste de toutes vos publications et conférences/cours etc., un résumé de 2 pages sur vos recherches ainsi que 2 à 4 lettres de recommandation.

Contact : Maxence Cassier, Philippe Briet et Thomas Ourmières-Bonafos.

Financement : CDD de 2 ans pris en charge par la fondation AMIDEX et l’Institut Archimède (Aix Marseille Université) - projet interdisciplinaire "Propagation in twisted waveguides"

Gestionnaire financier(e) en laboratoire H/F

Le/La gestionnaire réalisera les actes de gestion administrative dans le respect des techniques, dès règles et des procédures applicables au domaine de la gestion financière dans un contexte multi-tutelles (CNRS, Aix Marseille Université, École Centrale Marseille).

Type de contrat : CDD Administratif à temps complet de 6 mois renouvelables

Niveau d’études souhaité : Bac - Bac pro - Bac+2

Date d’embauche prévue : 1 septembre 2022

Rémunération : entre 1 799 et 1 962€ bruts mensuels selon expérience

Lieu : Institut Fresnel, Marseille

Contact : Émilie Carlotti, Responsable financière emilie.carlotti@fresnel.fr

 Voir les détails de l’Offre et Postuler

Post-Doctoral position in the development of X-ray texture tomography to study biomineralized tissue

The crystallographic texture is a major determinant for the behaviour of materials. Despite this importance, appropriate, quantitative methods to study the crystallographic texture in biomaterials in 3D are missing. In the framework of a project funded by the European Research Council (ERC Starting grant TexTOM), our group is aiming to develop texture tomography as a quantitative tool to study the crystallographic texture in 3D, based on previous work. We finally want to use it to study the mechanical behaviour of a functionally graded, hierarchically organized biomaterials, the bone-tendon insertion. This work is embedded in the larger research context of the COMiX team, whose expertise lies in the development of characterization techniques for complex crystalline materials with a specific focus on biomineralization.

Place : Institut Fresnel (Aix-Marseille University, CNRS, Ecole Centrale Marseille)
Duration : 36 months
Requirements :
 PhD degree with sound expertise in synchrotron science, scientific computation, X-ray diffraction, crystallography, biomineralization or a related discipline
 Very good knowledge in object-oriented programming, familiarity with Python is a bonus
 Highly-developed critical and analytical skills
 Capability to work in an interdisciplinary, international team

Application : Candidates are requested to submit a cover letter explaining shortly the relevance and motivation of the application, a detailed CV, 2 major publications and 3 academic references. Send it to tilman.grunewald@fresnel.fr

Postdoc Microscopie & Computational Imagerie

Le projet EquipEx+ IDEC "Computational Imaging and Detection" est coordonné par l’Institut Fresnel.
It focusses on the new generation of optical imaging and detection instruments based on innovative co-design, bridging instrumentation and computational approaches. In this context, Institut Fresnel brings together competencies in conceptual and numerical developments and in advanced instrumentation. A Postdoctorate level position is available in microscopy and computational imaging.
 The candidate will develop new fluorescence imaging microscopes for adaptive scanning and optimized polarized microscopy in collaboration with the research teams and Platform PHOTONICS members. The candidate will be in charge of the design based on existing proofs of principles, the implementation of these novel microscopy tools, and their operation in collaboration with partners from laboratories and industry, in particular in the field of cell and developmental biology.

Lieu : Institut Fresnel, Marseille, France
Dates : Début du contrat avant le 31 mars 2022
Durée : 24 mois
Contact : Sophie BRASSELET

Post-doc : Procédé de structuration et de polissage par laser CO2 de composants optiques en silice.

Ces dernières années, la fabrication de composants optiques a connu une évolution importante avec, d’une part la demande pour des optiques dites ‘free form’, c’est-à-dire dont la surface n’est ni plane ni sphérique, et d’autre part le développement de nouveaux procédés de fabrication tels que la structuration laser ou la fabrication additive. Les optiques ‘free form’ ou les optiques diffractives permettent de résoudre de nombreux problèmes de mise en forme de faisceaux laser.

Lieu : Institut Fresnel (Marseille) et CEA CESTA (Bordeaux) pour des missions ponctuelles
Conditions :disponibilité du poste en janvier 2022, durée 1 an renouvelable 1 an, salaire fonction de l’expérience du candidat.
References : https://www.researchgate.net/profile/Laurent-Gallais
Contact : Laurent GALLAIS

Post-doc Biomedical Optics

Development and validation of 3D signal
reconstruction algorithms for fluorescence
tomography in the second biological window
(SWIR)

Supervisor : Anabela Da Silva
+33 4 13 94 54 79
Email : anabela.dasilva@fresnel.fr
Team : DiMABio, Institut Fresnel/CERIMED
Place : Institut Fresnel, Av Escadrille Normandie-Niémen, 13397 Marseille Cedex 20

Post-doc imagerie biomédicale optique

Développement et validation d’algorithmes de reconstruction du
signal en 3D pour la tomographie de fluorescence dans la seconde
fenêtre biologique (SWIR)

Responsable : Anabela Da Silva
Tel : +33 4 13 94 54 79
Email : anabela.dasilva@fresnel.fr
Equipe : DiMABio, Institut Fresnel/CERIMED
Adresse : Institut Fresnel, Av Escadrille Normandie-Niémen, 13397 Marseille Cedex 20

Post-doc Proposal : High performance numerical modelling for nonlinear photonic devices

Post-doc Proposal : High performance numerical modelling for nonlinear photonic devices
Duration 12 months

Contact : herve.tortel@fresnel.fr

The work proposed, during this full-time 1-year, postdoctoral appointment is dedicated to the development of a 3D finite element software in order to study such kind of realistic configuration. Based on an already existing source code developed in our lab, the candidate will focus its future work in the implementation of new functionalities like :
 Use of high order basis functions dedicated to the scattering of 3D objects.
 The extension to the 3D case of domain decomposition techniques (FETI method [2]) and its application to anisotropic materials with the implementation of different types of local and global preconditioners.
 All the numerical developments will be considered as being used in a parallel environment.

A candidate with a PhD degree, preferably within the last 3 years, in Computer Science, Computational Sciences, Applied Mathematics, or a related technical field. A good expertise in Fortran/C and OpenMp/MPI programming is required.

The work will be performed in collaboration between the teams HIPE and CLARTE of Fresnel Institut .

CDD Gestionnaire de Parc Informatique

Gestionnaire de Parc Informatique - Niveau T ou AI selon profil - (12 mois renouvelable)

Profil de poste

Description des missions Intégré.e au sein du service informatique (5 personnes) de l’unité de recherche (190 personnes), le ou la gestionnaire du parc informatique assure le bon fonctionnement du parc et fournit une assistance aux utilisateurs dans la configuration et l’utilisation de leur poste de travail et des outils informatiques du parc, depuis la simple bureautique jusqu’aux ordinateurs de pilotage des bancs expérimentaux.