Diapositive 1

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European Intensive Seminars of Petrology, Paris
2007 State-of-the-art Analytical Imaging
techniques in Petrology
Use of Scanning Transmission X-Ray Microscopy in
Petrology
Theory and applications
Karim Benzerara karim.benzerara_at_impmc.jussieu.fr
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Outline
INTRODUCTION What is STXM in the Soft X-ray
range? Only few applications in Petrology so far
but clearly a state-of-the-art imaging
technique Keywords spectromicroscopy, chemical
speciation, 20-nm range, synchrotron
I. BASICS OF XANES SPECTROSCOPYAND OF
SPECTROMICROSCOPY
Optics
II. MICROSCOPE SET-UP
Sample stage
Requirements for sample prep
Detection
Sample environment
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III. EXAMPLES OF STXM APPLICATIONS TO PETROLOGY
HOW DOES IT WORK?
A. Carbon speciation geothermometer and search
for ancient traces of life - How to get images
and spectra by STXM -One example of sample
preparation FIB milling - Complementarity with
TEM
B. Quantification of Iron redox speciation and
mapping - Magnetite/maghemite - Mapping iron
redox in weathered basalts
C. Measurement of diffusion profiles in minerals
semi quantitative information - Detection limit
D. Polarization dependent imaging
,Textural/crystallographic information
CONCLUSIONS -Where and how to apply? -Review of
petrology projects done on STXM
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What is Scanning Transmission X-Ray Microscopy?
STXM in the Soft X-ray range capabilities and
limits are ? than those of STXM at e.g. ESRF
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Soft X-ray STXM performances
Provides unique combination of analytical
capabilities

• high Spatial Resolution

State of art 15 nm. Typically 30-40 nm
expect to reach 10 nm
Aknowledgements to Martin Obst (CLS) for this and
many other slides
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Comparison of spectromicroscopic techniques
QUANTITATIVE CHEMICAL ANALYSIS at relevant
spatial resolution
THE HOLY GRAIL of chemical microscopy
High
NMR
IR
RM
Chemical Information Content

XPS
TEM EELS
EDS
FM
SEM
OM
NSOM
TEM
STM
AFM
Low
100 mm
1 mm
10 nm
1 Å
Spatial Resolution
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Why using synchrotron light?
Monochromatic light
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Importance of TEM in petrology
A TEM study of carbon-rich grains in C chondrite
meteorites, Garvie and Buseck, EPSL 2004
A TEM study of the biotite-chlorite reaction,
Veblen Ferry, Am Min 1983
A TEM study of metal-silicate interaction, Leroux
et al., EPSL 2000
? TEM is a powerful technique to address a number
of issues but has few limitations e.g.
Ill-crystallized phases, contrast is not
chemistry-sensitive (except if EDX mapping or
STEM are run)
? Considering the high complementarity of STXM
with TEM STXM should become a useful tool in
petrology
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I. Basics of X-ray spectroscopy
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I. What information can we get from XANES spectra
?
1- Chemical composition (semi quantitative)
XANES can be applied to each core level of the
target
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I. What are soft X-rays ?
N.B There are few STXMs working with hard X-rays
and spatial resolutions of 50-100 nm
from David AttwoodSoft X-Rays and Extreme
Ultraviolet Radiation Principles and Applications
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I. What elements can be studied using Soft X-rays
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I. Basics of X- ray spectromicroscopy
Spectromicroscopy Both spectroscopy and
microscopy at high spatial resolution
Image contrast Differential absorption of
X-rays depending on speciation
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II. Microscope Setup Lets get deeper into the
microscope
Advanced Light Source synchrotron (Berkeley, CA)
from outside
synchrotron
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Microscope Setup
Lets get deeper into the microscope
Monochromating device
Ring
Microscope
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STXM 11.0.2 _at_ the Advanced Light Source (Berkeley)
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Scanning Transmission X-ray Microscope
STXM chamber
Fresnel lens zone plate (Au or Ni on Si3N4)
He, air or vacuum
Si3N4 Window
scanned sample
y
detector
x
x-rays
OSA
Focal length 0.5 15 mm (energy dependent)
OSA Order Sorting Aperture
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Zone plates Diffractive optics for X-ray
Non-uniformly spaced X-ray opaque Au rings on
X-ray transparent substrate (15 transmission)
SEM image of a ZP and its zone profile
Diameter 50 200 mm

Concentric rings (zones) with zone width
decreasing with radius focuses x-rays to a
point Spatial resolution equal approx. Outermost
zone width Focal length proportional to
energy Nanofabrication with E-beam lithography
Zone widths presently as small as 15 nm Working
distance 150 mm
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performance
December 2003 - improved ZP technology !

• 25 nm diffraction limited zone plates
• Recent advances in CXRO zone plate fabrication
• improved zone plates for STXM. Better
• spatial resolution
• - due to narrower outer most zones (25 nm
  instead of 35 nm)
• performance at high photon energy (up to 2500
  eV)
• - due to higher aspect ratio (71 instead of
  31)

25 nm 11 lines as test object
2005 15 nm
100 nm
15 nm
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Schematic of STXM components mechanical stages
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Low vibration a key to high resolution
Relative vibrations of sample and zone plate
measured with an interferometer 10 nm
M. Howells, C. Jacobsen, and T. Warwick,
Principles and applications of zone plate x-ray
microscopes, in The Science of Microscopy, ed.
P. Hawkesand J. Spence, KluwerPress (anticipated
2007).
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Sample Holder
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History of soft X-ray STXM
1985-90 initial development at Daresbury
(Michette), NSLS (Kirz) 1990 - STXM II at
X1A NSLS Kirz, Jacobsen 1992 Ade first
NEXAFS / polymer application (NSLS)
1995 - first STXM at the Advanced Light
Source (undulator line 7.0)
1997 NCSU-Dow-McMaster consortium
dedicated BM STXM - interferometer to
enhance chemical precision - user friendly
- optimized for materials analysis (C,N,O)
2001 (June 20) first image (Aug 08) first
remote operation from McMaster 2002 (July 1)
commissioned now STXM532 is highest demand
bend magnet line at ALS 2003 BL 11.0.2
undulator STXM commissioned (EPU, wide E-range)
now BL 1102 is highest demand undulator line
at ALS (largely due to STXM) 2006 - STXM532
clones begin operating at CLS, SLS under
development
at SSRL, Bessy
under consideration at Soleil, Diamond, NSLS-II
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III. Applications of Soft X-ray STXM in
Petrology A. Use of carbon in Petrology ?
Geothermometer ? Finding ancient traces of life
Classically Raman microspectroscopy? Quantifying
the Organization Degree of OM
Defect Band
Graphite Band
Geothermometer based on the relative area of the
defect band Beyssac et al. (2002) J. Metamorphic
Geology, 20, 859-871
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Carbonaceous plant fossils from La
VanoiseTriassic aluminous metasediments
unitsVanoise Massif - Western Alps (France)
Sylvain Bernard PhD, ENS Paris
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Mineral assemblage Mg-carpholite -
Fe-chloritoïde - Quartz - Phengite Paragonite -
Pyrophyllite Lawsonite - Cookéite - Aragonite
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A. Raman Spectroscopy Characterization of the
plant fossils
D. Band
G. Band
OM of Vanoise Structurally homogeneous - Maximum
temperature of 360C
Raman Shift (cm-1)
Raman spectrum of Vanoise OM
Bernard S. et al. Exceptional preservation of
fossils plant spores in high-pressure metamorphic
rocks. EPSL, 262, 257-272.
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Raman Mapping of associated Mineralogy
Bernard S. et al. EPSL, 262, 257-272
(Fe,Mg)Ca(CO3)2
Metamorphic phyllosilicate
CaCO3
Carbonates Zonation Ankerite corona beneath the
carbonaceous spore wall For further
characterization of megaspore wall OM down to the
nm scale ? TEM
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A. Sample preparation for STXM Focused Ion Beam
ultrathin sections extracted from spore wall
100 µm
SEM image
Carbonaceous Spore Wall
Inner area of the spore
5 µm
FIB image
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A. STXM analysis of the carbonaceous cell wall of
a metamorphosed spore from La Vanoise
Acquisition of an image below the C K-edge
01
scanning
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Playing with different energies for imaging
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A. Mapping of organic carbon/ carbonates.
O.D288 O.D280 map of C absorbing at 288 eV
organic C
Scale bar is 5 mm
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A. Spectroscopy Point scan
-log(I1/I0)
200 ms/point/energy, i.e. around 30 s at the same
point Risk of beam damage if sample is sensitive
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A. Spectroscopy Linescan
Now, I1 is measured on several points instead of
a single one, so the total time measurement per
point is reduced.
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A. Spectroscopy Image Stack
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A. Now, we have a XANES spectrum for each pixel
of the image
34200 points on this image! Difficult to analyse
by hand all those data
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Principal Component Analysis Spatial distribution
of various carbons in the spore wall
How to deal with this complexity? Pattern
recognition algorithms (PCA then
clustering) Lerotic et al. Ultramicroscopy 100,
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Graphitic Carbon
Metamorphosed Sporopollenin
Ankerite
Ankerite (Fe,Mg)CO3
Metamorphosed Sporopollenin
Graphitic Carbon
500 nm
Spatial distribution at the nanometer scale
of Graphitic carbon vs Ketone/phenol/carboxyl
Carbon
Origin of these heterogeneities ?
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Everything can be done with one software
aXis2000 by Hitchcock group httpunicorn.mcmaster
.ca/aXis2000.html
aXis2000
(httpunicron.mcmaster.ca/aXis2000.html)
aXis2000 is free for non-commercial use
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A. What do we learn on this specific case of La
Vanoise?
Two chemically different Organic Material are
preserved despite metamorphism
Carbonaceous Map
Below C K edge
Carbonate Map
Bernard et al, EPSL (2007) 262, 257-272
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High complementarity TEM / STXM
STXM
Speciation of Carbon
STXM image _at_ 285 eV
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B. Speciation of Fe by STXM Indications on Fe
redox state
TEM diffraction From lattice spacings either
magnetite or maghemite
Only way to distinguish between those 2 phases at
this scale spectroscopy
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B. Speciation of Fe by STXM Indications on Fe
redox state
Reference Fe(II) and Fe(III) compounds
708 eV
709,8 eV
Fe(II) phase
Fe(III) phase
Energie, eV
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B. Iron redox state Using Fe L3 edge
TEM EELS Van Aken and Liebscher (2002) Phys
Chem Minerals
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B. How important is microbial impact on iron
oxidation within the seafloor?
Some say traces of microbial weathering
pervasive e.g. Tubular features in basalt glass
0.5 mm
Segmented Texture
20 mm
0.2 mm
Septae?
20 mm
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B. Inside the channels at the nm-scale TEM
observations
Channels are filled w. weathering minerals
smectite
Smectite (Fe,Mg)3Si4O100H2
200 nm
Benzerara et al., Earth Planet Sci Lett (2007)
260, 187-200
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B. Fe oxidation state by XANES using the Fe L3
edge
NEXAFS _at_ Fe L3 edge (705 eV)
708 eV
710 eV

Reference Fe2
Volcanic glass Fe2
Channel Fe2 Fe3
Reference Fe3
700
704
708
712
716
Energy (eV)
Benzerara et al., EPSL (2007)
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C. Quantitative analysis of concentrations
measurement of diffusion profiles Vielzeuf et al.
2007 Contrib. Mineral. Petrol. 154, 153-170
Concentration gradients in calcium are common in
metamorphic or magmatic garnets and can be used
to determine the timescales of geological
processes. However, the kinetics of Ca diffusion
in garnet is poorly constrained and experimental
studies have to date yielded widely varying
diffusion coefficients.
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C. Absorbance (OD) ? concentration
349.2 eV
Ca L2,3 edges
344 eV
Vielzeuf et al.
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C. The same can be done for multi elements
Fe Map
708.3
Fe L2,3 edges
Diffusion profile
702
Vielzeuf et al.
Caution One should check that this is not
related to variations in thickness of the FIB
section !
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D. Dependency of absorption on the linear
polarization of light
3,5
1s?s
3
1s?p
E? c
2,5
2
1,5
1
E ?? c
0,5
0
280
285
290
295
300
305
Linear polarization of light
or
By changing the linear polarization of light and
measuring absorption, we can get information on
the crystallographic orientation of some
crystals. Here aragonite
See Ade and Hsiao, Science (1993)
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D. How stromatolites are built up by the growth
of aragonite crystals What crystallographic
patterns? Control by organic carbon?...
Smectite lamina
Aragonite lamina
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D. From stack analysis on a FIB section
aragonite is pervasive, but variations in the s/p
peak ratio
290.3 eV
Aragonite lamina
x 1
290.3 eV
Smectite lamina inclusions of carbonates
x 2
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D. Polarization dependent imaging Textural/crystal
lographic information
Linearly polarized X-rays can be used to probe
the orientation of chemical bonds in
non-isotropic samples
2 mm
All _at_ 290.3 eV
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CONCLUSIONS Soft X-ray microscopy where?
ALS, Berkeley 2 STXM 1 bending magnet (250-700
eV), 1 undulator (80-2100 eV)
Bessy-II, Berlin 1 STXM on an undulator (250-600
eV)
NSLS, Brookhaven 2 STXM 1 bending magnet
(250-500 eV), 1 undulator (250-1000 eV)
PLS, Pohang 1 STXM undulator (100-1600 eV).
Elettra, Trieste STXM (TwinMic, 250-2000 eV)
SLS STXM on Pollux (X07DA), 260-1100 eV CLS
STXM 205-2000 eV Diamond Proposal for a
STXM Soleil STXM in constrcution
How to apply.
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Only very few papers in the Petrology field. Most
of existing papers polymer chemistry, magnetism,
environmental science
General M. Howells, C. Jacobsen, and T.
Warwick, in Science of Microscopy, edited by P.
W. Hawkes and J. C. H. Spence (Springer, Berlin,
2006), pp. 835926. H. Bluhm, et al. Soft X-ray
Microscopy and Spectroscopy at the Molecular
Environmental Science Beamline at the Advanced
Light Source, J. Electron Spectroscopy 150 (2005)
86-104 A.P. Hitchcock et al. Soft X-ray
microscopy of soft matter - hard information from
two softs, Surface Reviews and Letters, 9 (2002)
193-202. T Beetz et al., Soft X-ray Microscopy
at the NSLS, Synch. Rad. News, 16 11-15 (2003)
Of petrology, mineralogy interest C Boyce,
G Cody, M Feser, C Jacobsen, A Knoll, S Wirick,
Organic chemical differentiation within fossil
plant cell walls detected with x-ray
spectromicroscopy, Geology, 30 1039-1042 (2002)
G Flynn, L Keller, S Wirick, C Jacobsen, S
Sutton, Analysis of interplanetary dust particles
by soft and hard x-ray microscopy, J. Phys. IV,
104 367-372 (2003) G Flynn, L Keller, C
Jacobsen, S Wirick, An Assessment of the Amount
and Types of Organic Matter Contributed to the
Earth by Interplanetary Dust, Adv. Space Res.,
33 57-66 (2004) K. Benzerara, T.H. Yoon, N.
Menguy, T. Tyliszczak, and G.E. Brown, Jr.,
Nanoscale Environments Associated with
Bioweathering of a Meteoritic Mg-Fe Pyroxene
Proc. Natl. Acad. Sci. 102(4), 979-982 (2005). S
Sandford, J Aleon, C Alexander, T Araki, S Bajt,
G Baratts, J Borg, J Bradley, D Brownlee, et al.,
Organics Captured from Comet 81P/Wild2 by the
Stardust Spacecraft, Science, 314 1720-1724
(2006) D Brownlee, P Tsou, J Aléon, C Alexander,
T Araki, S Bajt, G Baratta, R Bastien, P Bland,
et al., Comet 81P/Wild 2 Under a Microscope,
Science, 314 1711 - 1716 (2006) P Haberstroh, J
Brandes, Y Gelinas, A Dickens, S Wirick, G Cody,
Chemical Composition of the Graphitic Black
Carbon Fraction in Riverine and Marine Sediments
at Submicron Scales using Carbon X-ray
Spectromicroscopy, Geochim. Cosmochim. Acta, 70
1483-1494 (2006) V Chanudet, M Filella,
Submicron Organic Matter in a Peri-alpine,
Ultra-oligotrphic Lake, Org. Geoch., 38
1146-1160 (2007) D Solomon, J Lehmann, J Thies,
T Schafer, B Liang, J Kinyangi, E Neves, J
Peterson, F Liuzao, J Skjemstad, Molecular
Signature and Sources of Biochemical
Recalcitrance of Organic C in Amazonian Dark
Earths, Geochim. Cosmochim. Acta, 71 2285-2298
(2007) K. Benzerara, N. Menguy, N.R. Banerjee,
T. Tyliszczak, F. Guyot and G.E. Brown, Jr.
(2007) Alteration of submarine basaltic glass
from the Ontong Java Plateau a STXM and TEM
study. Earth Planet. Sci. Lett. 260, 187-200. S.
Bernard, K. Benzerara, O. Beyssac, N. Menguy, F.
Guyot, G.E. Brown Jr., B. Goffé. Exceptional
preservation of fossils plant spores in
high-pressure metamorphic rocks. EPSL, 262,
257-272.
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Come to STXM.
Tough.
0000 Start of the experiment 1400 end of the
experiment Total running time 4h between
floodings, technical problems and earthquake
But rewarding
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