X-ray Fluorescence Microtomography
Matt Newville, GeoSoilEnviroCARS Steve Sutton
Consortium for Advanced Radiation Sources Mark Rivers
University of Chicago Peter Eng
Reconstruction of cross sections from a set of
Allows study of internal structure of objects
which cannot be sectioned
X-ray Fluorescence Microprobe
X-ray Fluorescence: Measure characteristic Element Specific: Elements with Z>16 can
x-ray emission lines from de-excitation of be seen at the APS, and it is usually easy to
electronic core levels for each atom. distinguish different elements.
Quantitative: precise and accurate
elemental abundances can be made. x-ray
interaction with matter well-understood.
Low Concentration: concentrations down
to a few ppm can be seen.
Natural Samples: samples can be in
solution, liquids, amorphous solids, soils,
aggregrates, plant roots, surfaces, etc.
Small Spot Size: measurements can be
made on samples down to a few microns in
Combined with Other Techniques:
XANES, EXAFS, XRD
GSECARS Fluorescence Microprobe/Microtomography
Sample x-y-z- stage: 1mm step sizes
mounted focusing mirrors
Optical microscope (10x to 50x) with video system
X-ray Tomography: Overview
Microscope Sample broad
objective Phosphor x-ray
X-ray computed microtomography (CMT) gives 3D images of the x-
ray attenuation coefficient within a sample.
At each angle, a 2D absorption image is collected. The angle is
rotated around in 1o steps through 180o, and the 3D image is
reconstructed with software.
Element-specific imaging can be done by acquiring tomograms
with incident energies above and below an absorption edge.
X-ray Fluorescence Tomography
Transmission Sample thin x-
Fluorescence x-ray tomography is done with a
• can collect multiple fluorescence lines.
pencil-beam scanned across the sample. The
sample is rotated around and translated in x. • data collection is relatively slow.
Transmission x-rays are can be measured as well to • can be complicated by self-absorption.
give an overall density tomograph.
G.F. Rust, and J. Weigelt IEEE TRANSACTIONS ON NUCLEAR SCIENCE, 75, pp 14 (1998)
A. Simionovici, et al. in Developments in X-Ray Tomography II, SPIE Proceedings 3772, 304-310 (1999)
A. Simionovici, et al, Nuclear Instruments and Methods in Physics Research A, 467-468, pp 889-892 (2001)
C. G. Schroer, Applied Physics Letters, 79 (12), 1912-1914 (2001)
X-ray Fluorescence Tomography
Formally, the fluorescence intensity for a tomogram can be quite complex:
For atomic density for each element i. Here detector
is the absorption of the incident beam along the beam-path, and
is the absorption of the fluoresced beam along the path to the detector.
The self-absorption problem is fairly difficult to solve in general. At first,
we’ll stick to samples with low self-absorption. This (g = 1) means we can use
standard tomographic methods to convert data to elemental densities.
Fluorescence Tomography: Sinograms
The Raw fluorescence tomography data consists of
elemental fluorescence (uncorrected for self-absorption)
as a function of position and angle: a sinogram. This
data is reconstructed as a virtual slice through the sample
by a coordinate transformation of (x,) (x, y). The
process can be repeated at different z positions to give
Fluorescence Sinograms for Zn, Fe, and As collected
simultaneously for a section of contaminated root (photo,
right): x: 300mm in 5mm steps : 180 in 3 steps
Zn Fe As
Distributions of Heavy Metals in Roots
S. Fendorf, C. Hansel (Stanford): Toxic Metal around Root-borne Carbonate Nodules
The role of root-borne carbonate nodules in the
attenuation of contaminant metals in aquatic plants is
investigated with EXAFS, SEM and X-Ray fluorescence
These images of a 300 mm root cross-section (Phalaris
arundinacea) show Fe and Pb are uniformly distributed
in the root epidermis while Zn and Mn are correlated
with nodules. Arsenic is poorly correlated with the
epidermis, suggesting a non-precipitation incorporation.
Slicing the root would cause
enough damage that 2D
elemental maps would be
Such information about the
distribution of elements in the
interior of roots is nearly
impossible to get from x-y
photograph of root section
and reconstructed slices root
from fluorescent x-ray CT.
Interplanetary Dust Particles
G. J. Flynn (SUNY, Plattsburgh): Volatile elements in interplanetary dust
Interplanetary Dust Particles (IDPs) collected by
NASA aircraft from the Earth’s stratosphere allow
laboratory analysis of asteroidal and cometary dust.
MicroXRF analyses show enrichment of volatile
elements, suggesting the particles derive from parent
bodies more primitive than carbonaceous chondrites
(Flynn and Sutton, 1995). The IDP fluorescence
tomography images show that volatile elements (Zn
and Br) are not strongly surface-correlated,
suggesting that these elements are primarily
indigenous rather than from atmospheric
Fe and Ni impurities in synthetic diamond
Yue Meng (HP-CAT, Carnegie Institute of Washington)
Synthetic diamonds, grown in the presence of
molten Fe and Ni, tend to be rich in these metals.
Little is known about the chemical and spatial
distribution, but optical measurements indicated
that these metals were preferentially distributed
along different growth sectors (<100> and <111>,
for example) of ~100mm to 1mm sized diamonds.
We began with “normal” XRF intensity
measurements, moving the sample across the
beam along different growth faces (<111> shown),
and by doing Fe XAFS at selected spots.
We found that Ni is more homogeneously
distributed than Fe, and Fe is nearly pure FeO.
But: the penetration depth of 7-9KeV x-rays in
diamond is several hundred microns -- roughly
the depth of the diamond.
Fe XAFS for Fe inclusions in diamond
(blue) and for pure FeO (red).
Fe and Ni in synthetic diamond
Yue Meng (HP-CAT, Carnegie Institute of Washington)
photographs of <111> face
of diamond during collection
of fluorescence tomograms.
Sinograms of transmitted absorption coefficient mT and Fe and Ni fluorescence
intensities for synthetic diamond. Scans were taken with 4mm steps in x and
3 steps in .
The reconstructed slices (right) show one spot of very metal concentration,
several smaller Fe spots, and a broad distribution of Ni along the <111> faces.
Arsenic Distribution in Cattail Roots
Nicole Keon, Harold Hemond, Daniel Wells G&H
Typha root 2
Studying a Superfund site (Wells G+H
wetland) that gained notoriety in A Civil Action,
a reservoir of approximately 10 tons of arsenic 300 mm
within the upper 50 cm of the sediment profile.
Most of the arsenic is sequestered in the As Pb
wetland peat sediments with relatively little in
In contrast riverbed sediments in the wetland
(5 feet away) have higher concentrations of
aqueous (mobile) arsenic despite lower solid
phase concentrations. Cu Zn
Hypothesize that the metabolic activity of the
wetland plants may help to explain the
sequestration of arsenic in the wetland.
Oxidation State Tomograms
For assessing As contamination in roots, knowing the total elemental
concentration is not enough: the oxidation state is also desired.
By selecting the incident x-ray energy, we can preferentially select As3+ or As5+.
collected at 2
energies: at the
As3+ white line,
and well above
the edge, for total
Distribution of As3+ and As5+ in Cattail Roots
Nicole Keon, As3+ “As5+ ”
Daniel Brabander (MIT):
Weighted redox: As3+=43%; As5+=57%.
As3+/ As5+ is generally heterogeneous (boxed areas)
and there is a tendency for As5+ to be on the exterior
Trace Elements in Goffs Pluton Zircon
M. McWilliams (Stanford Univ)
Fluorescence CT of individual zircon crystals shows
the heterogeneities of U, Th, and Y in candidate
crystals for U-Pb dating. Zircons from Goffs Pluton
(Mojave) have Proterozoic cores and Cretaceous
overgrowths. The tomography images for a 150 mm
zircon show that the overgrowths are associated
with U and Th enrichment. The crystal contains a
large void (dark triangular feature). There is also
some U and Th "mineralization" within the void that
is zirconium-free (compare U and Zr images). The
yttrium distribution is quite heterogeneous with a
tendency of anti-correlation with Zr, U and Th.
Fluorescence CT in such a
strongly absorbing sample
(nearly all Zr!) is complicated by
reconstructions are the result of
a crude correction for self-
absorption in the sinograms.
Self Absorption in Zr sinogram
Uncorrected sinogram (detector viewing
from the right) for Zr fluorescence of
ZrSiO4. There is significant self-
absorption as seen by the decay of
intensity away from the detector.
The simplest self-absorption correction
to the sinogram uses a uniform
absorption coefficient of the sample,
and does a row-by-row correction.
This gives a more uniform density
across the sinogram and the
Sinograms and reconstructed slices for Zr
fluorescence from zircon: uncorrected (top) and
corrected (bottom) for self-absorption.
Self Absorption and reconstruction
As mentioned earlier, the self-absorption problem is fairly difficult to solve in
general, and can probably only be solved self-consistently.
Very recent work (C. G. Schroer, Applied Physics Letters 79, Sept 2001) has
reported a successful method for doing this.
A model for the density, , for each element i, is constructed and used to
generate a model sinogram Ii(x,) . The density is then adjusted until the model
sinogram matches the data.
We haven’t tried this yet, but hope to try this out…