Nanomaterial datasets to advance tomography in scanning transmission electron microscopy

Abstract 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. Metadata summary Design Type(s)reference design • nanomaterial structure generation objective Measurement Type(s)3D structure determination assay Technology Type(s)electron tomography Factor Type(s)Sample Characteristic(s) Download metadata file Machine-accessible metadata file describing the reported data (ISA-tab format) Background & Summary Electron tomography attempts to reconstruct 3D objects from 2D projection images taken at different viewing angles, or tilts—producing the entire internal structure of a specimen or region of interest. Since the first 3D reconstruction from electron micrographs1, tomography with the scanning transmission electron microscope (STEM) has been widely applied to nanoscale materials2,​3,​4,​5,​6,​7,​8,​9,​10,​11,​12. Utilizing the sub-angstrom 2D resolution of modern STEM, 3D reconstructions with sub-nanometre and even atomic detail have been demonstrated13,​14,​15,​16. In the design of advanced nanomaterials, 3D characterization of nano-scale structure offers valuable insight into a material’s macroscale function. As a result, demand for nanoscale STEM tomography is high17. Routine tomographic methods face several challenges that reduce final quality. The geometry of most specimens and specimen holders restricts tilt range to less than roughly 140°. Commonly referred to as ‘the missing wedge’, an incomplete tilt-range limits the information available for reconstruction and manifests as an elongation in the final reconstruction18,19. Contamination and specimen radiation sensitivity limit the number of viewing angles and the signal to noise, which in turn, restricts the final resolution in 3D20. Depth-of-field limits the maximum allowable size of the object that can be reconstructed; a particular problem for aberration corrected STEM13,21,22. Recently, efforts towards new reconstruction methods promise higher resolution reconstructions using fewer viewing angles and lower radiation doses than traditional reconstruction algorithms like Weighted Back Projection (WBP) and Simultaneous Iterative Reconstruction Technique (SIRT). New approaches such as the iterative Fourier-based equal slope tomography23 and compressed sensing inspired algorithms24,25 have demonstrated success in STEM tomography by improving reconstruction quality with reduced sampling. However, we still lack a fundamental understanding of when and how these algorithms fail. Adopting new algorithms into routine tomography requires thorough investigation17. A lack of high-quality, open access data is impeding development and validation of new algorithms and software for 3D reconstruction, visualization, and analysis. Currently, the best tomographic datasets are harboured by a privileged few. Researchers best suited for creating novel data processing and analysis techniques do not readily have access to experimental data. To address this deficiency, we present five datasets that have pushed the limits of electron tomography. Each dataset was acquired using a unique experimental technique, is of high quality, and contains materials with structural complexity: Tom_1) Tomography of Hyperbranched Co2P Nanoparticle: a 150° tomographic tilt series, taken at 2° increments. The Co2P nanocrystal has a complex morphology of bundled branches that resembles a six-pointed star26. This dataset represents a tilt range and increment typical of nano-scale STEM tomography. Tom_2) 180° Tomography of NPs on Nanofibre: a tilt series taken at 1° tilt increments over the full 180° tilt range of platinum nanoparticles on a graphitized carbon nanofibre support. This dataset provides a complete range of tilts, allowing researchers to better understand the effects of missing information. 16 fast acquisition images were acquired at each tilt, and the experimental signal-to-noise level can be adjusted by averaging different numbers of these images. Tom_3) Atomic Resolution Tomography of Pt NP: a 145° equal slope tomography tilt series of a single platinum nanoparticle, acquired at atomic resolution, enabling reconstruction of atomic features15. Tom_4) Atomic Resolution Tomography of Tungsten Needle: An equal slope tomography tilt series of the tip of a tungsten needle, acquired over the full 180° range, enabling atomic resolution reconstruction16. Tom_5) Through-Focal Tomography of Pt-Cu Catalyst: a 138° through-focal tomographic tilt series acquired in an aberration-corrected microscope of Pt-Cu fuel cell catalyst nanoparticles with a complex internal pore structure on an extended carbon support at 3° increments13. This dataset overcomes the limited depth of field that accompanies high-resolution aberration corrected imaging21 by combining through-focal sectioning and tilt-series tomography to reconstruct extended objects. The datasets include raw tilt series aligned for reconstruction and 3D reconstructions of each specimen—all in an easily readable TIF format. Combined, these datasets provide a standard, open set of test data for the growing field of tomographic reconstruction and visualization. The datasets allow researchers to rigorously test their algorithms from alignment to reconstruction on real experimental data. The datasets will also find a use as a training tool for scientists new to tomography, a validation tool for 3D tomographic visualization, and a template to seed a future open library of tomographic data. Methods In ADF-STEM electron tomography, a focused electron beam with sub-nanometre diameter is rastered across a sample of interest. Electrons scattered from the sample are recorded using an annular dark field detector, which generates a 2D projection image of the sample27,28. The viewing angle is changed by rotating the specimen and a series of projectio (...truncated)