EMC 2024
Simulating Experimentally Realistic iDPC Tomography of CeO2 Nanoparticles and Vacancies
On this page you will find additional information related to my work and my EMC2024 poster, and links to my references.
Background and Previous Work
The presented experimental simulations are a continuation of my work from last year, which I presented at MMC2023. This was a comparison of simulated HAADF and iDPC reconstructions of a CeO2 nanoparticle.
If you would like more detailed information about how to create HAADF and iDPC simulations with Python, I would suggest you also read my webpage on that poster. For information on how to create atomic models, please visit the ASE documentation. For information on TEM and STEM simulations, please visit the abTEM documentation.
Simulated Experimental Parameters applied via abTEM
Frozen Phonons
The frozen phonon model was applied to approximate the vibrations of atoms under the beam. A seed was used to ensure the same set of random vibrations were applied to each tilt series, providing a series of atom position configurations. I have generated the below figures to demonstrate the vibrations applied, showing both the overall and the cropped central region of my model. As adding more frozen phonon configurations adds significant time to the PRISM simulation, I tested to find the lowest number of configurations which formed an accurate approximation, and selected 20 configurations based on this.
Defocus
Using abTEM, the Contrast Transfer Function is used to describe and apply aberrations, including defocus to STEM simulations. A value of 80 Å was selected for tilt series simulations based on initial testing across a range of values. Additionally, this value reflects a typical level of defocus which may be applied during manual tilt series acquisition due to non-exact focusing. The defocus CTF was applied during the PRISM simulation, as part of the S-Matrix.
Current
Poisson noise was used to simulate the effects of electron dose on the sample, through post-processing of the images with the poisson_noise function. Due to the flux limitations to avoid reduction of CeO2 nanoparticles, the focus was on minimising dose whilst maintaining the ability to resolve oxygens.
Source Size
The effects of the size of the electron source was also applied in post processing, with gaussian noise through the corresponding gaussian_noise abTEM function. As this is determined by a microscope's electron gun, the value for this was taken from expected minimum value for the X-CFEG on the Spectra 200 (S)TEM at Cardiff University.
SIRT 20 iDPC Reconstructions
iDPC - infinite dose
iDPC - 5e4 dose
iDPC - 1e4 dose
iDPC - 5e3 dose
Producing iDPC Tomography Reconstruction and Slices with ASTRA Toolbox.
The SIRT reconstructions was created with ASTRA toolbox. The algorithm input was a stacked NumPy Array containing the tilt series and a linear array of corresponding angles. These have been processed into gifs for easy viewing. Please click the button below to find out more about the functionality of ASTRA Toolbox.
All reconstructions demonstrate the expected visual difference in grey value for low atomic number elements with iDPC tomography. Please note the above reconstruction slices have had brightness and contrast adjusted, to allow best visualisation of the effect of different doses on iDPC tomography. The notable changes between different doses show the increasing noise, and the changing variation of the oxygen intensity compared to the background.
As noted on my poster, the oxygen vacancy is present on slice 538, on the lower left surface of the nanoparticle from this view in all reconstructions. This is visible in the above gifs at approximately the halfway mark. Here you can observe the increasing difficulty in locating the vancancy as dose is reduced.
Initial Experimental Data
As mentioned on my poster within the future work section, next we look to apply the results of these simulations to guide experiments.
I am pleased to report initial iDPC tomography of CeO2 nanoparticles has been completed at Cardiff. Experiments will continue with an aim to refine and optimise the protocol to capture the most accurate reconstruction.
Summed Side View (XZ)
Summed Beam View (XY)
Archived Poster PDF
EAK Poster EMC2024.pdfThank you for visiting my poster!
References
From Poster:
Carlsson, A., Alexandrou, I., Yücelen, E., Bosch, E. G. T., & Lazić, I. (2018). Low Dose Imaging Using Simultaneous iDPC- and ADF-STEM for Beam Sensitive Crystalline Structures. Microscopy and Microanalysis, 24(S1), 122–123. https://doi.org/10.1017/S1431927618001101
Yücelen, E., Lazić, I., & Bosch, E. G. T. (2018). Phase contrast scanning transmission electron microscopy imaging of light and heavy atoms at the limit of contrast and resolution. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-20377-2
Johnston-Peck, A. C., DuChene, J. S., Roberts, A. D., Wei, W. D., & Herzing, A. A. (2016). Dose-rate-dependent damage of cerium dioxide in the scanning transmission electron microscope. Ultramicroscopy, 170, 1–9. https://doi.org/10.1016/j.ultramic.2016.07.002
Hjorth Larsen, A., Jørgen Mortensen, J., Blomqvist, J., Castelli, I. E., Christensen, R., Dułak, M., Friis, J., Groves, M. N., Hammer, B., Hargus, C., Hermes, E. D., Jennings, P. C., Bjerre Jensen, P., Kermode, J., Kitchin, J. R., Leonhard Kolsbjerg, E., Kubal, J., Kaasbjerg, K., Lysgaard, S., … Jacobsen, K. W. (2017). The atomic simulation environment—a Python library for working with atoms. Journal of Physics: Condensed Matter, 29(27), 273002. https://doi.org/10.1088/1361-648X/aa680e
Rahm, J., & Erhart, P. (2020). WulffPack: A Python package for Wulff constructions. Journal of Open Source Software, 5(45), 1944. https://doi.org/10.21105/joss.01944
Ophus, C. (2017). A fast image simulation algorithm for scanning transmission electron microscopy. Advanced Structural and Chemical Imaging, 3(1), 13. https://doi.org/10.1186/s40679-017-0046-1
Madsen, J., & Susi, T. (2020). abTEM: ab Initio Transmission Electron Microscopy Image Simulation. Microscopy and Microanalysis, 26(S2), 448–450. https://doi.org/10.1017/S1431927620014701
van Aarle, W., Palenstijn, W. J., de Beenhouwer, J., Altantzis, T., Bals, S., Batenburg, K. J., & Sijbers, J. (2015). The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography. Ultramicroscopy, 157, 35–47. https://doi.org/10.1016/j.ultramic.2015.05.002
Rasband, W.S., ImageJ, U. S. National Institutes of Health, Bethesda, Maryland, USA, https://imagej.nih.gov/ij/ , 1997-2018.