The research in this thesis is focused on tomographic reconstruction based on two imaging modalities in electron microscopy. The first modality is high angle annular dark field scanning... Show moreThe research in this thesis is focused on tomographic reconstruction based on two imaging modalities in electron microscopy. The first modality is high angle annular dark field scanning transmission microscopy (HAADF-STEM), and the second modality is energy-dispersive X-ray spectroscopy (EDS). In this Ph.D. thesis, we propose several approaches to pave the way for HAADF- STEM + EDS tomography: (1) the HAADF-EDS bimodal tomographic reconstruction technique, which is based on jointly modeling the consistency of the two imaging modalities; (2) TNV-regularized joined reconstruction which allows to incorporate the prior knowledge that common edges exist in the reconstructions from HAADF and EDS data respectively; (3) a set of algorithmic recipes to tailor various reconstruction algorithms for given experimental conditions and sample properties; (4) an algorithm for automatically correcting the nonlinear damping effects in HAADF-STEM tomographic data. Show less
Bleichrodt, F.; Leeuwen, T. van; Palenstijn, W.J.; Aarle, W. van; Sijbers, J.; Batenburg, K.J. 2016
Mathematical scripting languages are commonly used to develop new tomographic reconstruction algorithms. For large experimental datasets, high performance parallel (GPU) implementations are... Show moreMathematical scripting languages are commonly used to develop new tomographic reconstruction algorithms. For large experimental datasets, high performance parallel (GPU) implementations are essential, requiring a re-implementation of the algorithm using a language that is closer to the computing hardware. In this paper, we introduce a new MATLAB interface to the ASTRA toolbox, a high performance toolbox for building tomographic reconstruction algorithms. By exposing the ASTRA linear tomography operators through a standard MATLAB matrix syntax, existing and new reconstruction algorithms implemented in MATLAB can now be applied directly to large experimental datasets. This is achieved by using the Spot toolbox, which wraps external code for linear operations into MATLAB objects that can be used as matrices. We provide a series of examples that demonstrate how this Spot operator can be used in combination with existing algorithms implemented in MATLAB and how it can be used for rapid development of new algorithms, resulting in direct applicability to large-scale experimental datasets. Show less
