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Nanomaterial Datasets to Advance Tomography in Scanning Transmission Electron Microscopy


Nanomaterial Datasets to Advance Tomography in Scanning Transmission Electron Microscopy

Barnaby D A Levin et al. Sci Data.


Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co2P nanocrystal, platinum nanoparticles on a carbon nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.

Conflict of interest statement

The authors declare no competing financial interests.


Figure 1
Figure 1. Illustration of electron tomography data acquisition and reconstruction process.
Series of 2D images acquired of object of unknown 3D structure at different viewing angles. Images shown are from tiltser_Co2P.tif. 2D images combined into image stack ordered by viewing angle i.e., a tilt series. Tilt series is aligned, and reconstruction algorithm is applied to produce 3D reconstruction of object. A 3D isosurface visualization of recon_Co2P.tif is shown as an example rendered using tomviz.
Figure 2
Figure 2. Illustrations of tilt series and sample reconstructions.
(a) Sample image from tiltser_180.tif. Mixed 3D volume/isosurface visualizations of recon_180.tif show exterior of fibre, with nanoparticles visible on exterior, and hollow interior of nanofibre, containing nanoparticles. (b) Sample image from tiltser_PtNP.tif. Mixed 3D volume/isosurface visualization of recon_PtNP.tif and volume visualization of 3D Fourier transform of recon_PtNP.tif, showing platinum reciprocal lattice spots. (c) Sample image from tiltser_W.tif. Mixed 3D volume and isosurface visualization of recon_W.tif and of the 3D Fourier transform (cropped) of recon_W.tif, showing tungsten reciprocal lattice spots. All 3D visualizations produced using tomviz.
Figure 3
Figure 3. Illustration of raw data and sample reconstruction for Tom_5.
A through-focal image series must be acquired at each viewing angle in through-focal tomography. Files 018.tif, 072.tif, and 120.tif are shown as examples. Through-focal tomography allows objects from an extended field of view to be reconstructed at high resolution in an aberration corrected STEM. A 3D isosurface visualization of the full view of PtCu nanoparticles on an extended carbon support in recon_ThroughFocal.tif is shown, along with high resolution 3D visualizations of individual PtCu particles in the reconstruction. All visualizations produced using tomviz.

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Data Citations

    1. Levin B. D. A.. Figshare. 2016 - DOI


    1. DeRosier D. J. & Klug A. Reconstruction of Three Dimensional Structures from Electron Micrographs. Nature 217, 130–134 (1968). - PubMed
    1. Weyland M., Midgley P. A. & Thomas J. M. Electron Tomography of Nanoparticle Catalysts on Porous Supports: A New Technique Based on Rutherford Scattering. J. Phys. Chem. B 105, 7882–7886 (2001).
    1. Inoue T. et al. Electron tomography of embedded semiconductor quantum dot. Applied Physics Letters 92, 031902 (2008).
    1. Koguchi M. et al. Three-dimensional STEM for observing nanostructures. J. Electron Microscopy (Tokyo) 50, 235–241 (2001). - PubMed
    1. Saghi Z., Xu X. & Möbus G. Three-dimensional metrology and fractal analysis of dendritic nanostructures. Physical Review B 78, 205428 (2008).

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