Transfer of tilted sample information in transmission electron microscopy

Mariani, Valerio. Transfer of tilted sample information in transmission electron microscopy. 2010, Doctoral Thesis, University of Basel, Faculty of Science.


Official URL: http://edoc.unibas.ch/diss/DissB_9193

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When a transmission electron microscope is used in imaging mode, information carried by
the sample function is transformed by the optics of the instrument during the imaging process.
A mathematical description of this physical process (the so-called imaging function)
is a requirement for an accurate analysis and the interpretation of electron microscopy
experimental data. When the sample is not imaged in tilted geometry (no defocus gradient
is present across its extent), the imaging function has a well-known and extensively
studied form : the Contrast Transfer Function (CTF) (Reimer, 1997). Several
electron microscopy techniques, however, require the sample to be tilted to fully
explore its 3-dimensional structure. Only recently a rigorous mathematical description
for the imaging process under these conditions, derived from physical
first principles, has been made available: the Tilted Contrast Imaging Function
(TCIF) (Philippsen et al., 2006).
The present work discusses in depth the nature and the characteristics of the TCIF model,
expanding it to include astigmatism. A robust and efficient software implementation is
presented, developed with the context of the IPLT software development framework
(Philippsen et al., 2007). Computer simulations of images of tilted samples are then
used to qualitatively and quantitatively analyze features of experimental images.
No computationally-feasible analytical method for the inversion of the TCIF model
is currently available, and its effects on experimental images are usually corrected using
a number of heuristic methods that involve some approximations of the imaging parameters.
Using computer simulations of tilted images, this work estimates the errors introduced
by these approximations, and suggests optimal correction strategies for electron tomography
and crystallography imaging conditions. Furthermore, this work describes possible approaches
for the determination of the imaging parameters through the analysis of the experimental images,
and for a non-analytical inversion of the effects of the TCIF model, showing preliminary
results of their implementation applied to computer simulated-images.
Reimer, L. (1997). Transmission Electron Microscopy. Physics of Image Formation
and Microanalysis. Springer-Verlag GmbH, 4. A. edition.
Philippsen, A., Engel, H. and Engel, A. (2006). The contrast-imaging function
for tilted specimens. Ultramicroscopy, 107(2-3):202–12.
Philippsen, A., Schenk, A. D., Signorell, G. A., Mariani, V. and Berneche, S.et al.
(2007). Collaborative EM image processing with the IPLT image processing
library and toolbox. Journal of Structural Biology, 157(1):28–37.
Advisors:Engel, Andreas
Committee Members:Stahlberg, Henning
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Former Organization Units Biozentrum > Structural Biology (Engel)
UniBasel Contributors:Stahlberg, Henning
Item Type:Thesis
Thesis Subtype:Doctoral Thesis
Thesis no:9193
Thesis status:Complete
Number of Pages:175 s.
Identification Number:
edoc DOI:
Last Modified:22 Jan 2018 15:51
Deposited On:20 Oct 2010 11:52

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