Description du sujet de thèse

The thesis is part of a collaboration between Laboratoire d'Études Spatiales et d'Instrumentation en Astrophysique (Lesia) and Institut de Biologie de l'École Normale Supérieure (Ibens).
The IBENS team seeks to understand how the nervous system ensures cognitive functions and controls animal behavior. They record images showing the simultaneous activity of large populations of neurons, or even the entire brain for zebrafish larvae which are an excellent vertebrate model in neurobiology. Tracking large neuronal populations with cellular resolution and good temporal resolution remains a technical challenge though.


The LESIA team has been working for years on the development of innovative adaptive optics systems for large ground-based telescopes such as the Very Large Telescope (8 meters in diameter), the Extremely Large Telescope (39 meters in diameter) or biological imaging. Hardware and software solutions developed in adaptive optics for astronomy, and which have proven themselves in this field, should be adaptable to closed-loop microscopy at a frequency compatible with the experimental constraints (photo-bleaching, use with awake animals).

The thesis project is divided into three stages:
1. Characterize optical aberrations and study scattering introduced by samples such as clarified mouse brain slices, or zebrafish larvae. Study the dependence in the field, the transition regime between aberrations and diffusion, etc. The measurements will be carried out with techniques and instrumentation adapted to the characteristics of the biological tissues.
2. Define the best wavefront analyzer and strategy of use (where to measure aberrations, at what time frequency, etc.) for light sheet fluorescence microscopy.

3. Design and build in the laboratory an adaptive optics device optimized for light sheet fluorescence microscopy.

The progress of the thesis will not be so linear. There will be back and forth between digital model and laboratory demonstration. The imaging device will initially be a simple full-field imager in epifluorescence allowing the imaging of a 2D fluorescent object to which will be added aberrant or scattering objects. This will make it possible to have optical sectioning inherent in the sample, to measure and correct aberrations on emission, to have a certain flexibility in varying the parameters of interest (level of aberrations, wavelength, source consistency).

Activités
The PhD student will define and lead the studies by numerical simulations and laboratory demonstrations. His work will be based on an existing formalism of the propagation of light in scattering media of inhomogeneous optical index and absorption.
The results will be published in peer-reviewed journals and presented at international conferences.

The PhD student will thus carry out parametric studies in the laboratory as well as in numerical simulation. Then, the system will evolve into a light sheet microscope to observe 3D objects (clarified brain slices, zebrafish larvae) with an adaptive optics wavefront sensor at emission and a correction at emission and excitation. The final system will be able to equip microscopes used at Ibens for neuroscience research.

Compétences
+ geometric optics and physical optics, in particular in light sheet fluorescence microscopy and adaptive optics.
+ system engineering

Contexte de travail

The thesis will mainly take place at the Meudon site of the Paris-PSL Observatory The PhD student will be part of the biological imaging team of Lesia. This team is composed of a teacher-researcher, an astronomer and two engineers. The team, like the PhD student, is part of the High Angular Resolution in Astrophysics (HRAA) team (50 persons). The PhD student will be invited to the HRAA seminars as well as to the PhD days of the laboratory.

The PhD student will work with one of the engineers of the biological team every day. He will have a weekly meeting with the Lesia thesis director. As soon as the PhD needs it, broader meetings, including the Lesia biological imaging team and Ibens collaborators (2 researchers), will be organized.

The PhD student, accompanied by the Lesia team if needed, will regularly visit Ibens to ensure that the instrumental choices are consistent with the scientific objectives of the teams of biologists.

The PhD student will be employed by the CNRS for 3 years and enrolled in the Doctoral School 127 of astronomy and astrophysics.

Contraintes et risques

None