Presentazione di PowerPoint

6/22/2015
Tecniche di imaging con luce di sincrotrone per lo
studio dei geomateriali: dalla radiografia alla
tomografia computerizzata a 4 dimensioni
Lucia MANCINI
Elettra - Sincrotrone Trieste S.C.p.A.
34149 Basovizza (Trieste) – Italy
The Synchrotron Light
Beamline
Beamline
The electromagnetic radiation generated by charged particles, typically electrons
or positrons, traveling through magnetic fields at speed very close to the speed of
light. The frequencies generated can range over the entire electromagnetic
spectrum.
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SYRMEP: the imaging beamline @ Elettra
The SYRMEP beamline @ Elettra
Designed and constructed in collaboration with the Trieste section of INFN
and the Physics Dept. of Università di Trieste. Devoted to the development
and application of hard X-ray imaging techniques.
Medical applications
- in vitro and ex-vivo experiments  bones, tissues, teeth, drugs, ...
-in-vivo studies
 small animals
 mammography
Material science studies
- microstructural features
 in a very large range of materials
- purpose
 relationships with physical properties
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The SYRMEP beamline layout
ionization
chamber
air slits
Elettra
bending
magnet
v acuum
s lits
double Si(111)
monochromator
sample
stage
detector
 Energy range: 8.3 38 keV, Bandwidth E/E  2x10-3
 Beam size at sample (h x v)  160 mm x 5-6 mm
 Source size (FWHM) s (h x v)  230 mm x 80 mm
 Typical fluxes @15 keV  7 * 108 phot./mm2 s (@ 2.4 GeV, 180 mA)
 Source-to-sample distance: D  23 m
Why hard X-ray imaging at a 3rd generation SR facility?
 high energy photons and high flux
 heavy and/or bulky samples in transmission geometry
 tunability in a large energy range (optimization, artefacts - dose reduction)
 short exposure times (scan duration, real time)

small angular source size and big source-to-sample distance
 high spatial resolution (r = s d / D < 1 mm @ SYRMEP)
 possibility of big sample-to-detector distances (d < 1 m)
 high spatial coherence of the X beam (Lc = l D/(2 s)  10 µm @15keV)
Phase-sensitive techniques
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Absorption and Phase-Contrast radiography
detector
Synchrotron
source
D
detector
Refractive index: n = 1 -   i 
d
Fresnel diffraction
sample
n = 1 -  - i : refraction index
d0
Absorption contrast: due to differences in
absorption of X–rays in the object
d  0.1 1 m
Phase contrast: due to refraction of X-rays
in the object
(P. Cloetens, ESRF
France)
Free-space propagation
PC Regimes
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Phase vs. Amplitude effects with hard X-rays
(by P. Cloetens, ESRF, France)
Gain up to a few 1000!
Phase-contrast could be observed also when absorption-contrast undetectable
Images of a Mimosa flower (D. Dreossi & co.)
@ 10 keV
Absorption image
Phase-contrast image
@ 25 keV
Absorption image
Phase-contrast image
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Radiographs of an AlPdMn grain recorded at the ESRF (France)
Mancini L., PhD Thesis, 1998
Mancini L. et al., Phil. Mag. A 78 (1998) 1175
Absorption radiograph
Phase radiograph
E = 35.5 keV
lamellae
holes
200 mm
Lezard
~3 cm
E = 17 keV
d = 50 cm
Courtesy of A. Astolfo
SYRMEP
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Synchrotron X-ray computed microtomography (m -CT)
CCD camera
Sample
PC
Scintillator Screen
y
d
q
z
White or monochromatic
X-ray beam
x
Sample Stage
Planar Radiographs
 Precious for investigation of internal features without sample sectioning:
 in many cases the sectioning procedure modifies the sample structure
 the sample can be after studied by other experimental techniques,
 or submitted to several treatments (mechanical, thermal, etc...)
SYRMEP: mCT setup, detectors & optics
Photonic Science HYSTAR



16 bit, 2048 x 2048 pixels2
pixel size: (3.85) 14 x
(3.85) 14 mm2
FOV: (8) 28 mm x (8) 28
mm
Photonic Science VHR



12 bit, 4008 x 2672 pixels2
effective pixel size:
4.5x4.5 mm2
FOV: 18 mm x 12 mm
Photonic Science Lenscoupled



16 bit, 2048 x 2048 pixels2
pixel size: 7.4x7.4 mm2
FOV: continuously
adjustable
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TomoLab: a cone-beam m-CT station @Elettra
TOMOLAB
Designed at Elettra and constructed in
collaboration with Dip. Ingegneria e
Architettura and Corso di Laurea in
Odontoiatria e Protesi Dentaria of the
Università of Trieste.
Source: V = 40÷130 kV, Pmax = 39 W,
focal spotmin = 5 mm
CCD camera: 12bit, pixel size = 12.5 µm,
FOVma= 50 mm x 33 mm
The ICTP-Elettra X-ray laboratory for
cultural heritage, archaeology and paleontology
Inside the facility
X-ray
sourc
e
Sample stage
Flat
panel
detect
or
Coordinator: Prof. Claudio Tuniz
Source: V = 40÷150 kV, Pmax=
75 W, focal spotmin = 5 mm
Detector: 12bit, pixel size = 50
µm, FOVma= 120 mm x 120 mm
C. Tuniz et al., NIM A , 711 (2013) 106-110
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Elaboration of tomographic images
Planar radiographs are elaborated by a reconstruction procedure
Reconstructed slices are then visualized:
 2D slices visualized as Stack
 3D views of the sample can be obtained (Volume rendering)
Lezard
Courtesy of S. Favretto
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Breast imaging: the SYRMA (SYnchrotron
Radiation for MAmmography) project
{Financed by Fondazione Cassa di Risparmio di Trieste}
Agreement among the Public Hospital of Trieste, the University of Trieste and Elettra
Aim: In vivo mammography studies on cases selected by Radiologist
Target:
dense breasts;
conventional radiographs with uncertain diagnosis.
Dose reduction
Improvement of the contrast resolution
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Phase-contrast
radiography
Biomaterials
Implanted bone
1 mm
E = 29 keV, d = 17 cm
Tesei L. et al., Nucl. Instrum. and Meth. A, 548 (2005) 257-263
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Food science
Bread crumb
Aerated chocolate
E = 12 keV
d = 20 cm
E = 13 keV
d = 6 cm
2 mm
1 mm
Voxel=(8x6.78x2.8) mm3
P.M. Falcone et al., Journal of Food Science 69 (2004) E39-E43
P.M. Falcone et al., Advances in Food and Nutrition Research 51 (2006), 205-263
Soft matter
Polymeric foams
Wood
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Non-destructive evaluation of ancient
musical instruments
Heat transfer in Aluminum metal foams
30 PPI
20 PPI
10 PPI
STL modeling and Computational Fluid Dynamics simulations
P. Ranut , E. Nobile, L. Mancini, Experimental Thermal and Fluid Science (2015)
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Paleontology
Pathological fossil snake vertebra (1 Ma. old)
M. Galiová, J. Kaiser et al., Analytical and Bioanalytical Chemistry, 398 (2010) 1095
Swiss Bee Research Centre
Bee trapped in Amber 20-40 Ma. old found
in the Dominican Republic
1 mm
E = 14 keV
d = 20 cm
# of proj. = 900
1 mm
Sagittal view of Proplebeia abdita
(Greco and Engel n. sp. holotype)
CB: central body of brain
RT: retinal zone of compound eyes
DM: direct flight muscles
IM: indirect flight muscles
RM: loaded rectum
1 mm
Greco M.K. et al., Insectes Sociaux, 8 (2011) 1-8
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Multi-phase systems
Human kidney stones
Cement-based materials
N. Marinoni et al., Journal of Material Science, 44 (2009) 5815-5823.
J. Kaiser et al., Urological Research, (2010), in press.
The Pore3D project: why?

A sw library specifically designed for X-ray μ-CT images of porous media
and multiphase systems, Manipulation of huge datasets with common hw.

Different strategies of analysis as a function of the scientific application:
Pore3D implements several algorithms for each step of the analysis, having
a full control of the parameters of the algorithm and of the intermediate
results.

On the basis of specific know-how of the SYRMEP collaboration the main
aim was to merge many of features implemented in existing software, in some
cases customizing it or adding new tools.
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The Pore3D software library @ Elettra
Pore3D is a tool for 3D image processing and analysis
Filters
Basic (mean, median, gaussian, ...)
Anisotropic diffusion
Bilateral
Ring artifacts reduction
Binary (median, clear border, ...)
Skeleton extraction
Thinning
Medial axis (LKC)
DOHT
Gradient Vector Flow
Skeleton pruning
Skeleton labeling
Segmentation
Automatic thresholding (Otsu, Kittler, ...)
Adaptive thresholding
Region growing
Multiphase thresholding
Clustering (k-means, k-medians, ...)
Morphological processing
Dilation and erosion
Morphological reconstruction
Watershed segmentation
Distance transform
H-Minima filter
http://www.elettra.eu/pore3d
Analysis
Minkowski functionals
Morphometric analysis
Anisotropy analysis
Blob analysis
Skeleton analysis
Textural analysis (fractal
dimension, ...)
F. Brun et al., NIM A, 615 (2010) 326–332
3D analysis of the canal network of Stylaster sp.
(Cnidaria, Hydrozoa) by means of X-ray mCT
Colony in situ
3D rendering of a branch
S. Puce et al., Zoomorphology, 130 (2011) 85-95
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Section of a branch without coenostem
DACTYLOPORE
AMPULLAE
THIN CANALS
GASTROPORE
TomoLab
Study of the growth process
Cyclosystem
Cyclosystem enlargement
Old and new gastropores
surrounded by a single ring
of dactylopores
Cyclosystems completely
separated
Analysis of coral’s transverse sections sequence shows:
 reciprocal relationship between adjacent cyclosystems
 each new cyclosystem buds between gastropore and dactylopores of last formed one
S. Puce et al., Coral Reefs, 31 (2012) 715-730
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m-CT imaging of multiphase flow in carbonates (core  5 mm)
Portland limestone
Indiana limestone
Middle Eastern carbonates
Guilting limestone
Mount Gambier limestone
M.J. Blunt et al., Advances in Water Resources, 51 (2013) 197-216.
S. Iglauer et al., Fuel, 103 (2013) 905-914.
Clashach sandstone: oil-water distribution
voxel size: 9 mm
3D distribution of brine (blue) and residual oil clusters (red)
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3D quantitative analysis of igneous rocks
Formation of a volcanic rock: a
complex process with many steps
involved, from magma ascent in the
conduit to fragmentation
and
emplacement beyond the crater's rim.
Products of explosive eruptions, such
as pumices and scoriae, feature an
arrangement of crystals and vesicles
within a glassy matrix. This
represents the status of the magma
prior to the fragmentation process;
then a great deal of information about
the history of the rock formation can
be obtained by the study of its
morphology and texture.
SYRMEP
Courtesy of M. Polacci (INGV, Pisa)
mCT images of a pumice rock from Ambrym volcano
Axial view
@ SYRMEP
pixel size = 9 μm
E = 28 keV
Sagittal and frontal slices
D.R. Baker, L. Mancini et al., Lithos, 148 (2012) 262-276
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3D movie of a pumice rock from Ambrym volcano
D.R. Baker, L. Mancini et al., Lithos, 148 (2012) 262-276
Scoria from Ambrym, moderately vesiculated, poorly crystallized
Abundance of isolated vesicles
Connected component analysis
Red: connected component
Yellow: the others
Vesicles isolated after watershed
segmentation and border
cleaning.
Vesicles -> 50 %
Scoria from Stromboli, poorly to moderately vesiculated, highly crystallized
Blue: pyroxene crystals
Yellow: feldspar crystals
vesicles -> 36 %
pyroxenes -> 28%
feldspars -> 12%,
D. Zandomeneghi et al., Geosphere, 6 (2010) 793-804
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Scoria from Etna (experiments performed at the TOMCAT
beamline at the Swiss Synchrotron Light Source, PSI)
feldspars
pyroxenes
voxel size: 1.85 μm
oxides
vesicles -> 68.9%, plagioclases -> 4.3%, pyroxenes -> 3.2%, “oxides” -> 0.7%, glass -> 22.9%
22.9%.
M. Voltolini et al., J. of Volc. and Geothermal Res., 202 (2011) 83-95
But …. more complicated samples
A synthetic trachyte sample obtained by crystallization experiments (under
controlled conditions of pressure, temperature and time) in water-saturated
conditions starting from material of Campi Flegrei (Italy). Small crystals of
alkali feldspars embedded in a glass matrix: one of the most complicated
cases to perform image segmentation because of their similar density and
chemical composition.
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The phase-retrieval
approach
Phase retrieval
Back projection
Computed tomography
reconstruction
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Synthetic trachyte sample (material from Campi Flegrei)
Reconstructed axial slice
F. Arzilli, L. Mancini, et al., Lithos, 216-217 (2015) 93-105
Reconstructed axial slice
after phase-retrieval
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3D segmentation and separation of alkali-feldspar spherulites
F. Arzilli, L. Mancini et al., Lithos, 216-217 (2015) 93-105
3D visualization of a alkali-feldspar spherulite
F. Arzilli, L. Mancini et al., Lithos, 216-217 (2015) 93-105
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3D Shape Preferred Orientation (SPO) analyses
In the Pole Figures the long,
medium and short axes of
the ellipsoids used for fitting
the single lamella are
plotted.
F. Arzilli et al., Lithos, 216-217 (2015) 93-105
A 4D X-ray tomographic microscopy study of
bubble growth in basaltic foam
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TOMCAT beamline at the Swiss Light Source (Villigen)
Laser
Microscope
and CMOS
camera
Sample spindle
4D movie of the bubble growth
 Hydrated glasses (3 and 7 wt.%
H2O content) heated by a laser
furnace to above glass transition,
~600°C, in < 30 s.
As T increased to ~1200°C, full
3D data sets collected every
second for 18 s.
 Rapidity of heating simulates
instantaneous decompression.
D.R. Baker et al., Nature Communications, 3 (2012) 1135
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Skeletonization to measure bubble and pore throat sizes
in a volcanic rock ((3 wt.% of dissolved H2O)
a)
b)
c)
a) Topology preserving skeleton with nodes (red) at the intersections of the branches
(yellow).
b) Maximal inscribed spheres to calculate bubble volumes.
c) Maximal inscribed spheres to calculate pore throat diameters and wall thicknesses.
D.R. Baker et al., Nature Communications, 3 (2012) 1135
Experiments vs. natural Bubble Size Distributions
4D experiments
D.R. Baker et al., Nature
Comm., 3 (2012) 1135
Normal Strombolian eruption
Paroxysmal eruption
Polacci et al., J. of Geophysical Research, 114 (2009) B01206
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Conclusions
Many topics in petrology, volcanology, structural geology,
sedimentology and paleontology can be afforded by using 3D-4D CT
imaging combined with quantitative image analysis and complementary
techniques (electron and X-ray micro-analysis, neutron imaging and
diffraction, ….)
Spatial
resolution
Info
to extract
Beamtime
availability
Sample
damage
Sample size/
material
Grazie per l’attenzione
Vi aspettiamo @ Elettra!
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E grazie a ….
 A. Abrami, F. Arzilli, F. Brun, K. Casarin, V. Chenda, A. Curri, D. Dreossi, C.
Fava, G. Kourousias, E. Larsson, S. Mohammadi, R.H. Menk, R. Pugliese, N.
Sodini, G. Tromba, A. Vascotto, F. Zanini (Elettra – Sincrotrone Trieste , Italy)
 F. Arfelli, M. Biasotto, E. Castelli, R. di Lenarda, R. Longo, E. Nobile, P. Ranut,
L. Rigon, G. Schena, G. Turco (Università di Trieste)
 M. Polacci, P. Landi (INGV Pisa, Italy), D. Giordano (Univ. of Torino, Italy)
 M. Rivers (CARS, Univ. of Chicago, USA)
 D.R. Baker, A. La Rue, C. O'Shaughnessy (McGill Univ. of Montréal, Canada)
 D. Morgavi, D. Perugini (Univ. of Perugia, Italy)
 M. Voltolini (Lawrence Berkeley National Lab., California, USA)
 D.B. Dingwell (LMU – Munich, Germany)
 A. Bernasconi, N.. Marinoni, A. Pavese, P. Vignola (Univ. of Milano, Italy)
 J. L. Fife, F. Marone (SLS, Villigen, Switzerland)
 C. Pritchard, P. Larson (Washington University, USA)
 F. Bernardini, M.L. Crespo, C. Tuniz, C. Zanolli (ICTP, Trieste)
 L. Bondioli, A. Coppa, R. Macchiarelli (Univ. Roma, Univ. Poitiers)
 G. Bavestrello, D. Pica, S. Puce (Università di Ancona, Italy)
 M. Galiová, M. Holá, J. Kaiser (Brno Univ. of Technology, Czech Republic
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