Adaptive optics for quantitative confocal microscopy

Type d’annonce: Proposition – Postes CDD

Description de la proposition:

TECHNOLOGY TRANSFER PROJECT – CONFOBRIGHT

Adaptive optics for quantitative confocal microscopy

Suitable candidate: engineer or PhD in optics experienced in advanced microscopy

The resolution of fluorescence microscopy is often limited by the aberrations introduced by the biological sample when imaging deep into thick tissues. Indeed, the sample distorts the incident and radiated fields, thereby degrading the image formation. It is possible, however, as what is done in astronomy (where aberrations are due to atmospheric turbulences), to correct the wave front, using, for example, a deformable mirror: this is the principle of Adaptive Optics (AO).
A new approach, adapted to confocal microscopy, has been proposed at the Interdisciplinary Physics Laboratory (LIPhy) and Institut for Advanced Biosciences (IAB) from 2011. While, in general, certain characteristics of the image (such as the intensity or the contrast) are used to measure the impact of the deformation of the wave front, the new strategy implementation takes advantage of the temporal fluctuations of fluorescence due to the small number of molecules diffusing through the confocal volume. Indeed, it is possible to calculate, from these fluctuations, quantities such as the average number of molecules in the confocal volume, or their brightness (that is to say, the signal per molecule)1. It should be mentioned that most of the time confocal microscopy of biological living specimens does not allow direct measurement of the wave front. In fact, measuring a quantity such as brightness is equivalent to measure the signal from a single guide star and thus allows access to the Strehl ratio. This principle has already been demonstrated in the frame of a former ANR (National Agency for Research) Emergence project (2012- mid 2014) and led to several publications about biological applications and one patent2,3,4.
The Confobright projects aims first at setting-up on the IAB platform a quantitative confocal microscope equipped to perform fluorescence fluctuation measurements with an adaptive optics add-on. In contrast to the initial home-made system built at the LIPhy laboratory, the IAB prototype will be based on commercial only solutions. The quantitative confocal microscope will be provided by a company with whom we are collaborating, while the choice of the adaptive optics add-on is currently under investigation. The software developments necessary to drive the deformable mirror will be done with the technical support of the microscopy company. Along with these technical developments, a series of biological applications will be investigated on the IAB platform to assess and optimize the performances of the AO-quantitative confocal microscope in various experimental conditions. The project will run for 18 months, with the financial support of the Technology transfer & start-up building company of Grenoble Alpes.
We are seeking for a talented engineer and/or PhD, with a strong experience in advanced microscopy and willing to work at the interface between physics and biology. Knowledges in confocal microscopy, adaptive optics, photon correlation and control software are especially welcome. The position is available from January-February 2017.

Proposé par: Antoine DELON
Email: antoine.delon@univ-grenoble-alpes.fr

Laboratoire/Institution: Laboratoire Interdisciplinaire de Physique (LIPhy) et Institut for Advanced Biosciences (IAB)
Adresse: LIPhy, Université Grenoble Alpes, Pôle Phitem CS 40 700, Cedex 9, Grenoble, 38058, France
Details en pdf: http://gdr-miv.fr/gdr/wp-content/uploads/formidable/Ingeneering-offer-AO-1618-ang.pdf

Engineer/PostDoc in computer science for microscopy

Type d’annonce: Proposition – Postes CDD

Description de la proposition:

Team: Quantitative Imaging of the Cell
Type of contract: 12 months, renewable, full time
M.S/PhD in a computer science, bioinformatics or biotechnology
Salary: commensurate with experience
Characteristic duties
We are searching a motivated engineer/postdoc to create and expand on existing software solutions dedicated to biologists’ needs for the acquisition and analysis of High Content Screening (HCS) experiments on super-resolution optical microscopes.
Under the responsibility of the project leader and in close collaboration with the biology and bioinformatics teams, he/she will:
– Develop the software and graphical user interface for the acquisition (screening) and create a database from super-resolution microscopic image analysis (localizations, tracking, …)
– Implement new classification methods and evaluate them on biological data.
Requirements
– Language: Visual Basic .NET, C/C++. Optional: Python, Matlab, Java, R.
– Database IT, SQL.
– Knowledge of fundamentals of microscopy (Experience with Metamorph is a plus).
– Excellent communication skills, openness, and ability to collaborate in an interdisciplinary environment.
The team
The “Quantitative Imaging of the Cell” team develops novel imaging techniques to better understand the living cell activity at high spatial and temporal resolutions, in a high throughput context. The team works in close collaboration with the biology teams of IINS, the Bordeaux Bioinformatics Center (CBiB) and some industrial partners
Contact
Jean-Baptiste Sibarita: jean-baptiste.sibarita@u-bordeaux2.fr

Proposé par: Anne BEGHIN
Email: anne.beghin@u-bordeaux.fr

Laboratoire/Institution: IINS CNRS UMR 5297
Adresse: Bât PGF Université Bordeaux 2 146 rue Léo Saignat, Bordeaux, 33077, France
Details en pdf: http://gdr-miv.fr/gdr/wp-content/uploads/formidable/Offre-de-poste-info-IINS_englishpostdoc.pdf

Engineer Position in Image Analysis, Montpellier

Type d’annonce: Proposition – Postes CDD

Description de la proposition:

During development of a multicellular organism, precise control of gene expression allows the reproducible establishment of patterns that will lead to the formation of tissues and organs at the right time in the right place. While numerous studies have established how the spatial information is achieved and integrated, less is known concerning the temporal features of transcriptional control. Our goal is to understand how a precise temporal coordination in gene expression leads to accurate cell fate decisions during development. These questions are addressed the Drosophila embryo, a model system which allows quantitative imaging and genetic manipulations.
Mission
• The recruited engineer will work on the identification of the mechanisms leading to coordination in transcription during Drosophila embryogenesis. Towards this end, he/she will quantitatively analyze the transcriptional dynamics of key genes, monitored in living embryos with the MS2 labeling technique (see an example in the early embryo here).
• The engineer will collaborate with biologists of the team and interact with mathematicians for modeling projects.

Proposé par: Mounia Lagha
Email: mounia.lagha@igmm.cnrs.fr
Website: http://laghalab.com
Laboratoire/Institution: Institut de Génétique Moléculaire de Montpellier CNRS-UMR 5535 –
Adresse: 1919 route de Mende, Montpellier, 34293, France
Details en pdf: http://gdr-miv.fr/gdr/wp-content/uploads/formidable/Engineer-position-bio-imaging.pdf

Engineer in computer science for microscopy at the Interdisciplinary Institute for Neuroscience

Type d’annonce: Proposition – Postes CDD

Description de la proposition:

We are searching a motivated engineer to create and expand on existing software solutions dedicated to biologists’ needs for the acquisition and analysis of High Content Screening (HCS) experiments on super-resolution optical microscopes.
Under the responsibility of the project leader and in close collaboration with the biology and bioinformatics teams, he/she will:
– Develop the software and graphical user interface for the acquisition (screening) and create a database from super-resolution microscopic image analysis (localizations, tracking, …)
– Implement new classification methods and evaluate them on biological data.

Proposé par: Jean Baptiste Sibarita
Email: jean-baptiste.sibarita@u-bordeaux.fr

Laboratoire/Institution: IINS CNRS UMR 5297
Adresse: Bât PGF Université Bordeaux 2 146 rue Léo Saignat, Bordeaux, 33077, France
Details en pdf: http://gdr-miv.fr/gdr/wp-content/uploads/formidable/Offre-de-poste-info-IINS_v4.pdf

Poste d’ingénieur en informatique pour la microscopie à Bordeaux

Type d’annonce: Proposition – Postes CDD

Description de la proposition:

Nous recherchons un ingénieur motivé afin d’élaborer des solutions logicielles adaptées aux besoins des biologistes permettant de réaliser du High Content Screening (HCS) sur des microscopes optiques à super-résolution par localisation de molécules individuelles.

Equipe Imagerie Cellulaire Quantitative
Type de contrat : CDD de 12 mois, renouvelable
Quotité de travail : Temps complet
Niveau d’études souhaité : Bac+3 à Bac+5 en informatique ou bioinformatique
Expérience souhaitée : 1 à 3 années
Rémunération : Niveau Ingénieur d’Etude, selon diplômes et expérience

Proposé par: Jean Baptiste SIBARITA
Email: jean-baptiste.sibarita@u-bordeaux.fr

Laboratoire/Institution: IINS CNRS UMR 5297
Adresse: Bât PGF Université Bordeaux 2 146 rue Léo Saignat, Bordeaux, 33077, France
Details en pdf: http://gdr-miv.fr/gdr/wp-content/uploads/formidable/Offre-de-poste-info-IINS_v3.pdf