COVER STORY

From 2D to 3D Chemical Analysis

on the µm- to cm-Scale
Combining µ‑XRF and SEM/EDS with Serial Sectioning

Fig. 1: Loss of information from a 3D volume to a 2D section.

For a long time, the world of microanalysis was 2-dimensional. Recently, atom probe tomography (APT)
and focused ion beam (FIB) serial sectioning (combined with other techniques) have become available for
the 3D chemical analysis of small structures (<100 nm for APT and <20 µm for FIB). The article below il-
lustrates, that the modern silicon drift detector (SDD) technology used in energy dispersive spectrometry
(EDS) on scanning electron microscopes (SEM) and in spatially resolved micro X-ray fluorescence (µ‑XRF)
makes it quite simple to obtain 3D chemical data of larger samples. The total time spent on such 3D re-
constructions (including the time spent on 2D map acquisition, grinding/ polishing and 3D data presen-
tation) is comparable to the time spent on a 3D-FIB dataset. Advances in data processing make “sample
digitalization” possible. This means that the sample can be almost completely polished away, but all the
chemical data is still recorded and can be presented as a virtual 3D data cube. How EDS and µ‑XRF com-
plement each other in 3D chemical analysis is also discussed below.
Fig. 2: Typical
detection limits of
µ‑XRF and SEM/
EDS. For µ‑XRF, a
Rh-tube source and
an oxide matrix
were assumed.
For SEM/EDS, a
sample composi-
tion with a mean
atomic number of
28 (copper plus
element of interest)
was assumed.
2D Versus 3D 3D Structural Information Versus 3D
Chemical Information
Imagine living in a 2-dimensional world.
A significant amount of information, es- Displaying internal structures of com-
pecially regarding the true size of ob- plex materials in 3D has become easier
jects, their actual shape and specific as technology has made significant ad-
arrangement, would be missing. Further- vances, for example in X-ray computed
more, the number of objects observed in tomography (CT). This technique is non-
a 2D image, defined as a plane within a destructive, but it mainly displays differ-
3-dimensional space, would most likely ences in phase densities. Revealing the
not be representative for the whole vol- actual 3D element distribution in a sam-
ume. All of these drawbacks are illus- ple on the millimeter to centimeter scale
trated in figure 1. is complicated because of the self-ab-
sorption of X-rays before they can leave
the sample surface. Any non-destructive
technique promising 3D element dis-
tribution data quickly reaches its lim-
its when it comes to sample size and
resolution.
Recent developments in silicon drift
detector (SDD) technology as well as in
signal and data processing have made
µ‑XRF and EDS much faster [1, 2]. This
enables the 3D chemical analysis of
larger samples (with internal struc-
tures ranging from µm to cm in size) in a
short amount of time. In order to obtain
reliable and quantitative results with
3D-µ-XRF and 3D-EDS, the sample has to
be sectioned (for example by a stepwise
grinding and polishing procedure). Ro-
bots have been developed for this kind of
serial sectioning [3, 4], as they can easily
deliver a fairly constant sectioning depth.
2D element distribution maps are ob-
tained at each sectioning step and then
a virtual 3D data cube is reconstructed
with 3D visualization software. Bruker’s
HyperMap* option makes it possible to
access each 2D map later on for re-ex-
amination and post-processing. There-
fore the fact that this is a destructive
technique is compensated by what can
be called “sample digitalization”.
The Benefit of Combining µ-XRF and
SEM/EDS
Whether it’s a ceramic, a metal alloy, a
semiconductor or a rock sample, most
analysts know that they need to combine
the results obtained with several analyti-
cal methods in order to completely un-
derstand the chemistry and structure
of a sample. This is mainly the case, be-

G.I.T. Imaging & Microscopy 2/2013 • 19

 COVER STORY
cause every analytical technique has ad-
vantages and disadvantages, but it also
helps reduce precious instrument analy-
sis time.
SEM/EDS and µ‑XRF are well-estab-
lished analytical methods that comple-
ment each other in many ways. When
it comes to spatial resolution, one can
clearly “see more” with SEM/EDS (20
nm – 0.8 µm) than with µ‑XRF (≤ 25
µm). On the other hand, large scan areas
can be covered much faster with µ‑XRF
than with SEM/EDS. Figure 2 shows typi-
cal curves with detection limits for both
techniques. For elements heavier than
calcium (Z = 20), µ‑XRF is more sensitive
than EDS.
Fig. 3: Photograph of the Gujba meteorite.
3D Chemical Analysis of a Meteorite
Sample
In this study, a meteorite sample (“Gu-
jba”, shown in fig. 3) was chosen to dem-
onstrate the gain of information from 2D
to 3D chemical analysis, as well as the
potential of combining µ‑XRF and EDS.
The rock contains various objects with
a wide range of sizes and structures:
larger rounded metal particles, silicate
spherules and fine-grained materials –
making it an ideal example.
Table 1 lists analytical details for
three 3D datasets derived from the Gujba
meteorite. Two datasets were obtained
with µ‑XRF using a Bruker M4 Tornado
and one dataset was obtained with a
Quantax EDS system using a XFlash
6|60 silicon drift detector. The 3D-µ‑XRF
dataset “Volume 1” almost covers the
complete meteorite sample (fig. 4a). A
selected volume of interest was exam-
ined with higher resolution using both,
3D-µ‑XRF (“Vol. 2”, fig. 4b) and 3D-EDS
(“EDS”, fig. 4c). For all three datasets,
2D element distribution maps were im-
ported into a software for 3D reconstruc-
tions**. Even though serial sectioning
was performed by manual grinding and
polishing, the total time spent to produce
the 3D-datasets is still comparable to the
20 • G.I.T. Imaging & Microscopy 2/2013
Fig. 4: 3D reconstructions of chemical data from the Gujba sample shown in figure 3. a) 3D-µ‑XRF
dataset “Volume 1”, b) 3D-µ‑XRF dataset “Volume 2” (4.82 x 4.84 x 1.78 mm), c) 3D-EDS dataset (3.84
mm x 1.92 mm x 80 µm). The 2D-EDS data was acquired as a mosaic of 3x2 maps as indicated by the
white lines. See table 1 for analytical details of all three datasets.
time typically spent on 3D-FIB serial sec-
tioning (combined with EDS or EBSD).
It has been suggested that the metal
particles and silicate spherules (“chon-
drules”) of the Gujba meteorite were
formed from a vapor-melt plume, gen-
erated by a major impact event between
two protoplanetary bodies about 4.563
Ga*** ago [5]. If this hypothesis is correct,
one would expect that all metal parti-
cles in the Gujba meteorite show a quite
uniform chemical composition. However,
the 3D-µ-XRF data in figure 4a and 4b
shows that the chemical composition of
the metal particles is in fact variable, su-
ggesting a more complex origin. At least
5 different types of metal particles are
present. They can be characterized by:
▪▪ their Ni content: low: ~5 wt %
(dark blue), intermediate: ~6.5 wt %
(medium blue) and high: ~8.2 wt %
(light blue)
and
▪▪ by the abundance, size and shape
of sulfide inclusions (red).
Many sulfide inclusions are smaller than
6 µm in size – this is where EDS is help-
ful. The better spatial resolution of the
3D-EDS dataset (fig. 4c) allows the vis-
ualization of the large number of small
sulfide grains present in some of the
metal particles. An example is the metal
particle on the right side of the 3D-µ‑XRF
“Volume 2” (area indicated by the yellow
arrow in fig. 4b) and the 3D-EDS dataset
(yellow arrow in fig. 4c). Furthermore,
only with EDS, bowl-shaped structures
can be resolved for some of the sulfides
found within the metal particle (green
arrows in fig. 4c). Next to the sulfide-
free edges of the metal particle a lot of
sulfides are evident within the surround-
ing impact melt matrix (white arrows in
fig. 4c) indicating their mobilization. With
the 3D datasets, we can not only visual-
ize the actual size and shape of the metal
particles better than in 2D. We can also
examine how the particles stick together
and grasp the magnitude of interactions
between them and the surrounding im-
pact melt matrix. Our 3D data shows that
at least one more (so-called “secondary”)
impact event had a significant effect on
the chemical and possibly also the iso-
topic properties of the Gujba meteorite.
Conclusions
Recent advances in silicon drift detector
technology combined with progress in
the automation of serial sectioning have
created a lot of potential for 3D chemi-
cal analysis with µ‑XRF and SEM/EDS.
The total time spent on obtaining the 3D
chemical data (including sample prep-
aration, 2D data acquisition and time
spent on the 3D reconstruction) is com-
parable to the time typically spent on se-
rial sectioning with FIB (in combination
with EDS or EBSD). However, the cov-
ered sample volumes are several orders
of magnitude larger than with FIB (about
20 x 15 x 5 µm are typical for FIB). Vol-
umes of up to 20 x 15 x 5 cm can be cov-
ered with µ‑XRF. Therefore, analytical
questions involving larger sample vol-
umes can easily be addressed with the
method described here.
 COVER STORY

Acknowledgements Tab. 1: Analytical details

We would like to thank Rhian H. Jones µ-XRF: Vol. 1 µ-XRF: Vol. 2 EDS
(University of New Mexico, Albuquerque) Volume ~2200 mm³ 41.5 mm³ 0.6 mm³
for providing a test sample at the begin-
Layers 36 38 21
ning and for all of her advice during this
study. Section depth ~148 µm ~48 µm ~4 µm
Total depth 5.18 mm 1.78 mm 80 µm
Voxel size 32 x 32 x 148 µm 6 x 6 x 48 µm 1.6 x 1.6 x 4 µm
References
Instruments M4 TORNADO M4 TORNADO QUANTAX with XFlash 6|60
[1] Fiorini C. et al.: Review of Scientific Instru-
ments 68(6):2461–2465 (1997)
HV 30 kV 30 kV 15 kV
[2] Ritchie N.W.M. et al.: Microscopy and Microa- Beam current 600 µA 600 µA 5 nA
nalysis 18(4):892–904 (2012) Input countrate ~150 kcps ~150 kcps ~130 kcps
[3] Alkemper J. and Voorhees P. W.: Journal of Mi-
Acquisition time per layer 80 min 60 min 90 min
croscopy 201:388–394 (2000)
[4] Spowart J.E.: Scripta Materialia 55:5–10
Grinding/sample prep time ~20 min ~15 min ~15 min
per layer
(2006)
[5] Krot A. N. et al.: Nature 436:989–992 (2005) Total time ~60 h ~50 h ~40 h

* HyperMap is Bruker’s version of position tagged

spectrometry (PTS), where a complete spectrum Authors Contact
is acquired and stored for each pixel of the map- Dr. Jana Bergholtz (maiden name: Berlin)
Dr. Jana Berlin,
ping, allowing offline analysis from the database Bruker Nano GmbH
Ulrich Waldschläger,
even after the sample is no longer available. Berlin, Germany
Dr. Roald Tagle
** Tel.: +49 30 670990748
VSG’s Amira was used here.
*** 
Fax: +49 30 67099030
Ga = gigaannum- a unit of time equal to
jana.bergholtz@bruker-nano.de
1,000,000,000 years. www.bruker.com
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G.I.T. Imaging & Microscopy 2/2013 • 21