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Updated: Apr 6, 2026

Preparation and Observation of Thick Biological Samples by Scanning Transmission Electron Tomography
Published on: March 12, 2017
Local sample thickness determination via scanning transmission electron microscopy defocus series
A Beyer1, R Straubinger1, J Belz1
1Materials Science Center and Faculty of Physics, Philipps-Universität Marburg, 35032, Marburg, Germany.
Abstract:
The usable aperture sizes in (scanning) transmission electron microscopy ((S)TEM) have significantly increased in the past decade due to the introduction of aberration correction. In parallel with the consequent increase of convergence angle the depth of focus has decreased severely and optical sectioning in the STEM became feasible. Here we apply STEM defocus series to derive the local sample thickness of a TEM sample. To this end experimental as well as simulated defocus series of thin Si foils were acquired. The systematic blurring of high resolution high angle annular dark field images is quantified by evaluating the standard deviation of the image intensity for each image of a defocus series. The derived dependencies exhibit a pronounced maximum at the optimum defocus and drop to a background value for higher or lower values. The full width half maximum (FWHM) of the curve is equal to the sample thickness above a minimum thickness given by the size of the used aperture and the chromatic aberration of the microscope. The thicknesses obtained from experimental defocus series applying the proposed method are in good agreement with the values derived from other established methods. The key advantages of this method compared to others are its high spatial resolution and that it does not involve any time consuming simulations.
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