MMC 2023 Poster Information
Simulating iDPC tomography for Ceria Nanoparticles
Winner of MMC 2023 EMAG Poster Competition - Best Student Poster
Tilt Series - Gifs of full data set
Simulated HAADF tilt series
Simulated iDPC tilt series
Producing HAADF and iDPC Tilt Series in abTEM
The tilt series for both iDPC and HAADF were taken from -75 to +75 degrees, producing 151 images, from abTEM PRISM simulations of a 3nm truncated octahedron Ceria model, at interpolation 2.
Viewing the gifs, you can observe how the cerium atoms as clearly shown in both, whilst the oxygen atoms are only clear throughout all angles in the iDPC tilt series.
Reconstruction Slices - Gifs of full data set
Simulated HAADF slices in Reconstruction
Simulated iDPC slices in Reconstruction
Producing Tomography Reconstruction and Slices with ASTRA Toolbox.
The reconstruction was created with ASTRA toolbox. First by taking a 3D NumPy Array with the whole tilt series in, and then processing it through the 3D SIRT algorithm with ASTRA Toolbox.
Viewing the gifs, initially it goes through the vacuum. After, you can observe how the HAADF slices go dark when the iDPC slices show the oxygen layers, whilst both are bright showing cerium layers, indicating a visually distinguishable increase in grey value for low atomic number elements with iDPC tomography.
Archived Poster PDF
EAK Poster MMC2023 - Simulating iDPC Tomography.pdfReferences
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
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.