PhD student M/F - Brain-wide mapping with color multiphoton microscopy

Job Description

Thesis Subject

In vertebrates, the anatomy and structure of the brain are established during early development, and any abnormalities during these crucial stages can lead to serious pathologies. However, the mechanisms shaping brain regions are still poorly understood, due to the technical difficulty of mapping opaque tissue at different development stages with sub-cellular precision. To address these questions, the Laboratory of Optics and Biosciences (LOB, Ecole Polytechnique, Palaiseau) has developed in collaboration with the Institute of Vision (IdV, Paris) an original platform for large-volume 3D microscopy of ex vivo mouse tissue, called chromatic multiphoton serial microscopy (ChroMS) (Abdeladim 2019, doi.org/10.1038/s41467-019-09552-9; Blanc 2023, doi.org/10.1021/acsphotonics.3c01104). This method is based on the combination of a color two-photon excitation method developed at the LOB, automated serial sectioning, and the 'brainbow' approach developed at the IdV allowing multicolor fluorescence labeling of mouse neurons according to their cell lineages. The team is currently pursuing the improvement of the technology and exploring novel applications.

Objectives:
A first objective will be to adapt tissue-clearing techniques for multimodal nonlinear imaging while preserving both the structural integrity of the biological specimens and the integrity of the optical signals generated by cleared tissues. Imaging deep within biological tissues remains challenging because of optical aberrations caused by spatial variations in the refractive index. These aberrations degrade image quality and hinder quantitative image analysis, even when serial sectioning approaches are employed. To address this limitation, an initial strategy will consist of homogenizing the refractive index of the tissue using water-soluble clearing and refractive index matching media, and evaluating the benefits of this approach for three-dimensional imaging.
The first year of the project will focus on optimizing the experimental protocols and developing metrology methods to quantify improvements in imaging depth, preservation of tissue architecture, and overall imaging performance compared with conventional serial sectioning approaches. The potential complementarity of these two strategies will also be investigated. Once the clearing protocol has been optimized, the candidate will characterize the residual optical aberrations associated with different clearing protocols and tissue types in order to identify the most appropriate aberration correction strategy. A complementary development will involve the implementation of either a spatial light modulator (SLM) or a deformable mirror to compensate for these residual aberrations. The resulting adaptive optics system will then be validated on the ChroMS microscope. The objective will be to determine the optimal correction strategies as a function of tissue type and imaging depth.
A second objective will be to exploit this platform for organ-scale mapping of intrinsic label-free nonlinear optical signals, including endogenous autofluorescence, second harmonic generation (SHG), and third harmonic generation (THG). The initial applications will focus on imaging the mouse brain and cardiac tissue.
In the longer term, the project aims to establish large-scale three-dimensional reference datasets from tissues at different developmental stages and to develop automated image analysis strategies capable of extracting quantitative information on cellular and tissue morphology. Particular emphasis will be placed on investigating the development of neuronal circuits located in optically challenging, highly myelinated regions of the mouse brain, such as the brainstem.

Profile:
The candidate should have a background in physics / experimental optics, knowledge in programming and image/signal processing, and a motivation to work in an interdisciplinary environment. The project will involve experimental multiphoton microscopy (laser alignment, data acquisition), data analysis, programming, and basic biological sample preparations.

Your Work Environment

The project will be carried out at the Optics and Biosciences Laboratory at École Polytechnique (Palaiseau) as part of the Advanced Microscopy team. The host team offers an interdisciplinary environment combining optics, computer science, and biology. The work will involve daily interactions with a group of ~3–4 people, as part of a microscopy team of ~25 people, as well as interactions with collaborators at the Institut de la Vision (Paris). École Polytechnique is located in the Paris-Saclay region and is easily accessible by public transportation from Paris. More information is available at https://www.ip-paris.fr. The candidate will join the doctoral school of the Institut Polytechnique de Paris in the field of physics.

Constraints and risks

Use of femtosecond lasere

Compensation and benefits

Compensation

2300 € gross monthly

Annual leave and RTT

44 jours

Remote Working practice and compensation

Pratique et indemnisation du TT

Transport

Prise en charge à 75% du coût et forfait mobilité durable jusqu’à 300€

About the offer

About the CNRS

The CNRS is a major player in fundamental research on a global scale. The CNRS is the only French organization active in all scientific fields. Its unique position as a multi-specialist allows it to bring together different disciplines to address the most important challenges of the contemporary world, in connection with the actors of change.

CNRS

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