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X-ray Fluorescence Microtomography
Matt Newville, GeoSoilEnviroCARS
Consortium for Advanced Radiation Sources
University of Chicago
Steve Sutton
Mark Rivers
Peter Eng
Reconstruction of cross sections from a set of
projections.
Allows study of internal structure of objects
which cannot be sectioned
Too valuable
Too fragile
Too time-consuming
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X-ray Fluorescence Microprobe
X-ray Fluorescence: Measure characteristic
x-ray emission lines from de-excitation of
electronic core levels for each atom.
Element Specific: Elements with Z>16 can
be seen at the APS, and it is usually easy to
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
size.
Combined with Other Techniques:
XANES, EXAFS, XRD
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GSECARS Fluorescence Microprobe/Microtomography
Sample x-y-z- stage: 1mm step sizes
Sample
mounted
on silica
fiber
Horizontal and
Vertical
Kirkpatrick-Baez
focusing mirrors
Fluorescence
detector:
multi-element
Ge detector
Optical microscope (10x to 50x) with video system
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X-ray Tomography: Overview
Microscope
objective
Sample
Phosphor
CCD
camera
broad
x-ray
beam
x-rays

Visible light
rotation stage
X-ray computed microtomography (CMT) gives 3D images of the xray 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.
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X-ray Fluorescence Tomography
Transmission
detector
fluoresced x-rays
Sample
thin xray
beam
transmitted x-rays

rotation stage
x
translation stage
Fluorescence x-ray tomography is done with a
pencil-beam scanned across the sample. The
sample is rotated around  and translated in x.
Transmission x-rays are can be measured as well to
give an overall density tomograph.
• can collect multiple fluorescence lines.
• data collection is relatively slow.
• can be complicated by self-absorption.
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)
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X-ray Fluorescence Tomography
Formally, the fluorescence intensity for a tomogram can be quite complex:
For atomic density
for each element i.
Here
detector
incident
is the absorption of the incident beam along the beam-path, and
beam
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.
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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
three-dimensional information.
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
x
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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
tomography.
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
compromised.
Such information about the
distribution of elements in the
interior of roots is nearly
impossible to get from x-y
mapping alone:
photograph of root section
and reconstructed slices root
from fluorescent x-ray CT.
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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
contamination
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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).
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Fe and Ni in synthetic diamond
Yue Meng (HP-CAT, Carnegie Institute of Washington)
mT
mT
Ni
photographs of <111> face
of diamond during collection
of fluorescence tomograms.
Fe
Ni
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.
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Fe
Arsenic Distribution in Cattail Roots
Nicole Keon, Harold Hemond, Daniel
Brabander (MIT):
Wells G&H
Typha root 2
Fe
Studying a Superfund site (Wells G+H
wetland) that gained notoriety in A Civil Action,
a reservoir of approximately 10 tons of arsenic
within the upper 50 cm of the sediment profile.
Most of the arsenic is sequestered in the
wetland peat sediments with relatively little in
the groundwater.
In contrast riverbed sediments in the wetland
(5 feet away) have higher concentrations of
aqueous (mobile) arsenic despite lower solid
phase concentrations.
Hypothesize that the metabolic activity of the
wetland plants may help to explain the
sequestration of arsenic in the wetland.
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300 mm
As
Pb
Cu
Zn
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+.
E3 E5
Tomograms were
collected
at
2
energies: at the
As3+
white line,
and
well above
the edge, for total
As concentration.
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ET
Distribution of As3+ and As5+ in Cattail Roots
Nicole Keon,
Daniel Brabander (MIT):
As3+
“As5+
”
As total
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
(circled area).
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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
self-absorption.
These
reconstructions are the result of
a crude correction for selfabsorption in the sinograms.
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Self Absorption in Zr sinogram
Uncorrected sinogram (detector viewing
from the right) for Zr fluorescence of
ZrSiO4. There is
significant selfabsorption 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
reconstructed slice.
Sinograms and reconstructed slices for Zr
fluorescence from zircon: uncorrected (top) and
corrected (bottom) for self-absorption.
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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…
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