BER Structural Biology and Imaging Resources
Synchrotron, Neutron, and Cryo-EM
U.S. Department of Energy | Office of Science | Office of Biological and Environmental Research

X-Ray Fluorescence Imaging

Spatially-resolved images of chemical species within a sample

Two-dimensional X-ray fluorescence image of total Fe (a) and As (b) in a whole mount of a Fe plaque-free rice root grown in well-weathered soil. Panels (c–h) are higher resolution images of the yellow box in panel (a) that show the Fe (c), arsenite (As(III)) (d), and arsenate (As(V)i) (e) distribution where a lateral root has formed from the main root, and panels (f–h) are tricolor plots that show the localization of As(III) in relation to As(V)i and Fe (f), K (g), and S (h). All colormap units are in pg cm−2, with a maximum of 200 for Fe and 0.75 for As, and show that lateral root junctions are hotspots of As(III)i entering the vascular tissue. [Seyfferth, A. L., et al. 2017.]


X-ray fluorescence imaging (XRF), or x-ray spectromicroscopy, maps the distributions of elements and chemical species of interest within biological samples. Synchrotron XRF (SXRF) can provide detailed images of element speciation to a resolution of 0.5 µm per pixel, a sensitivity beyond desktop XRF, electron microprobe, or other elemental imaging techniques. SXRF resources supported by the DOE Office of Biological and Environmental Research (BER) can image phosphorus through most elements in the periodic table. Sample requirements and preparation are minimal, allowing the flexibility to explore diverse scientific questions and to design unique user experiments. SXRF beamlines use a combination of methods, ranging from mapping an area at a particular x-ray energy (that corresponds to the excitation of an element) to identifying the oxidation state and chemistry of a particular element using a technique called x-ray absorption near edge structure (XANES) spectroscopy.

Key Features of XRF Imaging

  • Chemical speciation mapping (beyond total elemental composition)
  • Imaging resolution tailored to sample size and scientific question (250 to 0.5 µm spot size)
  • Energy range of 2 to 25 keV for measuring phosphorus through technetium, and the possibility of additional higher-atomic-number elements
  • Accommodation of diverse sample types, including cells, organisms, soil, and rock
  • Diverse sample mounting forms
  • Simultaneous collection of multiple-element data

BER Researchers Use XRF to Study:

See more examples in Science Highlights

Sample Considerations

  • Sample imaging environments are either a helium-purged atmosphere (for elements from phosphorous to scandium) or ambient air.
  • Sample topography should be no greater than the width of the desired spot size (beam diameter), especially when investigating low-Z (low atomic number) elements.
  • Samples may be any thickness, but x-ray penetration of the sample depends on the x-ray energy and sample density.
  • Samples must stay upright when mounted in the beam. During analysis, the sample will move, not the beam.
  • Samples that can be mounted on a standard microscope slide are generally applicable to most beamlines. Users should discuss unique sample dimensions with the beamline experts.

SXRF Beamlines at DOE User Facilities

Each beamline has unique characteristics. To determine the user facility and beamline best suited to your science questions, see additional information and beamline contacts at the links below.


Seyfferth, A. L., et al. 2017. “Evidence for the Root-Uptake of Arsenite at Lateral Root Junctions and Root Apices in Rice (Oryza sativa L.),” Soils 1(1), 3. DOI: 10.3390/soils1010003.