Three-Dimensional Coordinates of Individual Atoms in Materials Revealed by Electron Tomography
[Data, image reconstruction and data analysis source codes for R. Xu, C.-C. Chen, L. Wu, M. C. Scott, W. Theis, C. Ophus, M. Bartels, Y. Yang, H. Ramezani-Dakhel, M. R. Sawaya, H. Heinz, L. D. Marks, P. Ercius and J. Miao, ¡°Three-Dimensional Coordinates of Individual Atoms in Materials Revealed by Electron Tomography¡±, Nature Mater. 14, 1099-1103 (2015).]
Posted on September 21, 2015
In 1959, Richard Feynman challenged the electron microscopy community to locate the positions of individual atoms in substances. Although significant progress has been made with electron microscopy over the last 55 years, Feynman¡¯s challenge - 3D localization of the coordinates of atoms in substances without averaging or a priori knowledge of crystallinity - remained elusive. Recently, we reported, for the first time, the determination of the 3D coordinates of thousands of individual atoms and a point defect in a material with a precision of ~19 picometer, where the crystallinity of the sample is not assumed. From the coordinates of these individual atoms, we measured the atomic displacement field and the full strain tensor with a 3D resolution of 1 nm and a precision of 10-3, which were further verified by density functional theory calculations and molecular dynamics simulations. The ability to precisely localize the 3D coordinates of individual atoms in materials without assuming crystallinity, identify point defects in three dimensions, and measure the atomic displacement field and the full strain tensor is expected to transform our understanding of materials properties and functionality at the most fundamental scale.
To facilitate those who are interested in our method, we make the data, image reconstruction and data analysis source codes in Matlab freely available below.
1) Click here to download 62 raw experimental projections.
2) Click here to download the raw experimental data of the 0¡Æ and 180¡Æ projections before and after acquisition of the full tilt series.
6) Click here to download the traced 3D atomic model.
7) Click here to download the source code (main function: Position_Refine.m) to refine the atomic model. (Note: as described in the Methods section, the positions of <1% of the atoms was manually adjusted during the refinement, which has also been widely used in the refinement process in protein crystallography.)
8) Click here to download the final 3D atomic model after refinement.
If you use any of the above data and source codes in your publications and/or presentations, we request you cite our paper: R. Xu, C.-C. Chen, L. Wu, M. C. Scott, W. Theis, C. Ophus, M. Bartels, Y. Yang, H. Ramezani-Dakhel, M. R. Sawaya, H. Heinz, L. D. Marks, P. Ercius and J. Miao, ¡°Three-Dimensional Coordinates of Individual Atoms in Materials Revealed by Electron Tomography¡±, Nature Mater. 14, 1099-1103 (2015).
This document was prepared by Yongsoo Yang, Rui Xu, Li Wu, and John Miao in the Department of Physics & Astronomy and California NanoSystems Institute, University of California, Los Angeles, California, 90095, USA. Email: firstname.lastname@example.org.