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Développements méthodologiques et informatiques pour la microscopie électronique en transmission appliqués à des échantillons biologiques

Abstract : Transmission Electron Microscopy is a major tool for performing structural studies in biology. Some methods used for image sampling and analysis need to be improved in order to observe electron dose sensitive samples with good contrast and good signal to noise ratio. During this thesis, various methodological and computational approaches have been studied which aim to improve image quality. First, I evaluated the relevance of combining energy filtered imaging with the STEM mode. I show that this allows an improvement of the signal to noise ratio of images. Then, I devised an algorithm that generates an image from phase data. This approach allows improving the image contrast over direct imaging. The use of a phase plate and focal tilt series are both efficient tools to achieve this goal. While working on the software approach for processing of tilt series, we found that a qualitative result can be obtained from a single image. I developped the SPCI plugin for the ImageJ software. It allows processing between one and three focal images. My work involves optimization of the tomographic reconstruction process, including working with both alignment algorithms and reconstruction algorithms. I expose my studies on image alignment methods used on tilt series. These methods do rely on the use of key points and associated local descriptors. They have proved to be efficient to process images lacking fiducial markers. Finally, I propose a new unified algorithmic approach for 3D reconstruction of tomographic tilt series acquired with sparse sampling. I then derived another novel method that integrates the image alignment step in the process. Studies and developments will continue on both methods in futur work.
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Submitted on : Friday, May 22, 2020 - 6:18:23 PM
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Amandine Verguet. Développements méthodologiques et informatiques pour la microscopie électronique en transmission appliqués à des échantillons biologiques. Traitement du signal et de l'image [eess.SP]. Université Paris-Saclay, 2019. Français. ⟨NNT : 2019SACLS487⟩. ⟨tel-02615460⟩

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