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Reference : UMR7645-LAULAC-003
Workplace : PALAISEAU
Date of publication : Tuesday, June 8, 2021
Scientific Responsible name : Anatole CHESSEL
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 October 2021
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly
Description of the thesis topic
Recent developments in microscopy are leading to the imaging of larger and larger volumes at increasingly fine resolutions. A fundamental challenge in computational bioimaging is to link this type of data to the biological questions that motivate it, in order to advance our understanding of life. Recently, the Laboratory for Optics and Biosciences (LOB) at the Ecole Polytechnique - Institut Polytechnique de Paris published the ChroMS technique, allowing the acquisition of large volumes of fixed brain tissue by multi-color multi-photon microscopy. Several developmental neurobiology projects are underway that will take advantage of this technological advance, and we are looking for a student motivated by biological data science to carry out the analysis of these acquisitions, in close collaboration with the experimenters.
The work will be done in the framework of an interdisciplinary collaboration and will rely on previous work in the lab as well as various open software recently developed in the community. In particular, the goal will be to set up a processing chain adapted to segment large images of mouse cerebellum to advance our understanding of the formation, connectomics and function of this brain region.
The project will be carried out in the Laboratory for Optics and Biosciences at Ecole Polytechnique (Palaiseau) in the advanced microscopies team, and will be co-supervised by Anatole Chessel and Emmanuel Beaurepaire. The host team provides an interdisciplinary environment combining instrumental developments, algorithmic and computational developments, and biology. Ecole Polytechnique is located in the Paris-Saclay area, and is easily accessible by transport from Paris. The candidate will join the doctoral school of the Institut Polytechnique de Paris, in the field of biology or computer science, according to his choice and profile.
An ideal candidate has an M2 in applied mathematics/computer science/data science/computer vision or a related discipline, good programming skills in Python, and an interest in interdisciplinary collaboration. Biological knowledge or at least a genuine interest in biology would be desirable.
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