TFS-STEM: Combined tilt- and focal series for STEM tomography with a computational correction for beam blurring
Image and Language Processing, Computer Graphics and Visualisation, Human Computer Interaction, Ubiquitous and Wearable Computing
Final Report Abstract
The primary method currently used for obtaining insight into the threedimensional (3D) structure at the nanometer scale of unique samples from biology and materials science is tilt-series transmission electron microscopy (TEM). In this project, we attempted to establish combined tilt- and focal series (CTFS) as a new recording scheme for threedimensional (3D) scanning transmission electron microscopy (STEM) imaging. In this scheme, the specimen is rotated in relatively large tilt increments, and for every tilt direction, a through-focal series is recorded. A 3D volume is then reconstructed using adapted algorithms of computed tomography. Our research hypothesis was that CTFS STEM would lead to an increased resolution in the axial direction and thus to a more faithful representation of 3D shapes compared to conventional tilt series. Two further research hypotheses were also formulated, namely, the idea that prior information of the objects would improve the reconstruction, and that the reconstruction can be extended by incorporating a compensation for beam blurring. All tasks were completed as needed to test research hypothesis #1, namely the implementation of a resolution calculation method as needed to ptimize microscopy settings, the preparation of samples of varying thickness and with nanoparticles at various vertical positions, the acquisition of TFS STEM datasets and comparing tilt-series data sets, the development, testing and optimization of reconstruction software, and the measurement of the achieved resolution. However, it was concluded that TFS STEM did not achieve a better axial resolution than conventional tilt series, and the lateral resolution was about the same as expected, under all tested conditions, which were considered the most optimal conditions. Research question #1 was thus addressed, namely, what are the optimal recording settings for recording a CTFS? Also, research question #2 was answered, namely, what is the achievable resolution in lateral direction using a CTFS on a specimen of a given thickness. Research hypothesis #1 was disproven. It was decided to stop the research on CTFS STEM at this point, and instead focus on the improving the temporal resolution of STEM, which is another important topic in addition to improving the axial resolution of 3D STEM. We achieved the highest possible scanning image acquisition speed by eliminating the dead time induced by the beam flyback time combined combined with reducing the amount of scanning pixels via sparse imaging and reconstruction via inpainting. A novel strategy for fast STEM was thus developed, implemented, and successfully tested.
Publications
- Three-Dimensional Reconstruction of Combined Tilt- and Focal-Series Scanning Transmission Electron Microscopy data. Microscopy Conference, Berlin, Germany, Sept. 1-5, 2019
Ortega, E., Dahmen, T. & de Jonge, N.
- Analysis of the dose-limited spatial resolution in transmission electron microscopy. Microsc. Microanal. 26 (S2) 1216-1217, 2020
Ortega, E. & de Jonge, N.
(See online at https://doi.org/10.1017/S1431927620017365) - High temporal-resolution scanning transmission electron microscopy using sparse-serpentine scan pathways. Sci. Rep. 11, 22722-1-9, 2021
Ortega, E., Nicholls, D., Browning, N.D. & de Jonge, N.
(See online at https://doi.org/10.1038/s41598-021-02052-1) - Resolution models for energy-filtered TEM imaging over thick liquid or amorphous layers. Microsc. Microanal. 27(S1), 802-803, 2021
Ortega, E. & de Jonge, N.
(See online at https://doi.org/10.1017/S1431927621003184) - The influence of chromatic aberration on the dose-limited spatial resolution of transmission electron microscopy. Ultramicroscopy online, 113383, 2021
Ortega, E., Boothroyd, C. & de Jonge, N.
(See online at https://doi.org/10.1016/j.ultramic.2021.113383)
