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3D Chemical Mapping: Application of Scanning Transmission (Soft) X-ray Microscopy (STXM) in Combination with Angle-Scan Tomography in Bio-, Geo-, and Environmental Sciences

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Electron Microscopy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1117))

Abstract

The identification of environmental processes and mechanisms often requires information on the organochemical and inorganic composition of specimens at high spatial resolution. X-ray spectroscopy (XAS) performed in the soft X-ray range (100–2,200 eV) provides chemical speciation information for elements that are of high biogeochemical relevance such as carbon, nitrogen, and oxygen but also includes transition metals such as iron, manganese, or nickel. Synchrotron-based scanning transmission X-ray microscopy (STXM) combines XAS with high resolution mapping on the 20-nm scale. This provides two-dimensional (2D) quantitative information about the distribution of chemical species such as organic macromolecules, metals, or mineral phases within environmental samples. Furthermore, the combination of STXM with angle-scan tomography allows for three-dimensional (3D) spectromicroscopic analysis of bio-, geo-, or environmental samples. For the acquisition of STXM tomography data, the sample is rotated around an axis perpendicular to the X-ray beam. Various sample preparation approaches such as stripes cut from TEM grids or the preparation of wet cells allow for preparing environmentally relevant specimens in a dry or in a fully hydrated state for 2D and 3D STXM measurements. In this chapter we give a short overview about the principles of STXM, its application to environmental sciences, different preparation techniques, and the analysis and 3D reconstruction of STXM tomography data.

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Acknowledgements

We thank E. Swanner and F. Zeitvogel for proofreading of this manuscript. We thank also the beamline staff of the SM beamline at CLS for excellent support during the STXM measurements and Adam P. Hitchcock for discussion. The CLS is supported by NSERC, CIHR, NRC, the Province of Saskatchewan, WEDC, and the University of Saskatchewan. Furthermore, we thank the Geomicrobiology group Tuebingen of A. Kappler, E. Struve, and W. Kuerner for their valuable help. This work was funded by DFG Emmy-Noether program to M.O. (OB 362/1-1).

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  1. Center for Applied Geoscience, University of Tuebingen, Tuebingen, Germany

    Martin Obst & Gregor Schmid

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  1. Martin Obst
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  1. University of Western Australia, Crawley, Australia

    John Kuo

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Obst, M., Schmid, G. (2014). 3D Chemical Mapping: Application of Scanning Transmission (Soft) X-ray Microscopy (STXM) in Combination with Angle-Scan Tomography in Bio-, Geo-, and Environmental Sciences. In: Kuo, J. (eds) Electron Microscopy. Methods in Molecular Biology, vol 1117. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-776-1_34

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  • DOI: https://doi.org/10.1007/978-1-62703-776-1_34

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