Description du sujet de thèse

The PhD will use and further develop ptychography algorithms for transmission electron microscopy data. The candidate will join a multi institute research group working on ptychography being between the microscopy platform in CEA Grenoble and the transmission electron microscopy group at Institut Neel.
The aim of the work is to advance and automate the use of ptychography on various sample types. In particular:
1) accelerate the reconstruction process using a multislice algorithm
2) allow a 3D reconstruction and
3) automate the reconstruction process and stream line it for near live reconstruction and a simplified and improved user experience, to open this extremely powerfull technique to non-expert users and high throughput applications
The focus will lie on so-called multislice algorithms to obtain atomic resolution and three-dimensional phase images, that can be correlated with conventional tomography (by rotating the sample), focussing on accelerating and automating the reconstruction process. Three transmission electron microscopes will be available for the work, all equipped with either Medipix or Timepix direct detection cameras. Both institutes have cluster facilities for data treatment. The candidate can involve in the data acquisition and sample preparation, but the main focus will be the ptychographic data treatment and analysis. The samples can range from model systems like 2D materials or thin lamella of semiconducting samples, going closer to devices like phase-change random access memory (PCRAM) or electrodes in lithium-ion batteries samples as the project advances. The results of the ptychography will be correlated with both chemical as well as structural three dimensional analysis of the same sample.

Main activities: Optimize the acquisition parameters of 3D-Electron Ptychography (combining ptychography and a limited number of view directions, ie., tomography) and improve or further develop the reconstruction algorithm.
We will start from existing software, but may need to optimize the algorithm for electrons or reconstruction speed.
Activities will include:
- carrying out simulations of electron ptychography datasets,
- reconstructing data testing different algorithms using multi slice algorithms,
- adapting ptychography reconstruction algorithms,
- stream lining the ptychographic data analysis: accelerating the reconstruction, facilitating the reconstruction process.

Skills:
- Mathematical insight and curiosity in ptychography
- Experience, affinity or interest in ptychographic data reconstruction.
- Knowledge in programming, data treatment, electron diffraction simulations, mathematical skills, knowledge about machine learning and artificial intelligence is a plus.

Contexte de travail

Electron Ptychography (EP) has become the ultra-high resolution and low dose electron microcopy technique [Science 372, 826–831 (2021)]. The purpose of this PhD project is to further develop EP in Grenoble (France).
The candidate will be part of a national project METSA-SETDIA [https://www.cnrs.fr/en/pepr/pepr-exploratoire-diademe-materiaux] which aims to improve/accelerate 3D structural characterization of Nanostructures, allowing to open the technique to non-specialists.
The candidate will join a CNRS/CEA team composed of electron microscopists and software engineers. He/She will have access to enhanced computer clusters and state-of-the-art transmission electron microscopes (TEM) either located at institute NEEL (Neoarm + medipix camera) or CEA (Neorm + timepix3 camera or TITAN Ultimate + medipix camera).

The Institut NÉEL is a CNRS unit (UPR 2940) under agreement with the University Grenoble Alpes. It is one of the largest French national research institutes for fundamental research in condensed matter physics enriched by interdisciplinary activities at the interfaces with chemistry, engineering and biology. It consists of 450 employees, including 175 researchers.
It is located in Grenoble, in the heart of a unique scientific, industrial and cultural environment, right next to the French Alpes.
The PhD will join the MRS (Materials, radiations, structure) research team of the Physique LUmière Matière department of the Institut Néel.

Contraintes et risques

No particular constraints or risks are related to this work.