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6/22/2015
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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
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.
Beamline
Beamline
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SYRMEP: the imaging 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
The SYRMEP beamline @ Elettra
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Elettra b e n d i n g
m a g n e t
i o n i z a t i o n c h a m b e r
s a m p l e
v a c u u m s l i ts
detector
double Si(111)
monochromator
air slits
stage
The SYRMEP beamline layout
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
Refractive index: n = 1 - i
sample
d
detector
d 0.11 m
Synchrotron
source
D
detector
d 0
(P. Cloetens, ESRF
France)
Phase contrast: due to refraction of X-rays
in the object
Absorption contrast: due to differences in
absorption of X–rays in the object
Fresnel diffraction
n = 1 - - i : refraction index
PC Regimes
Free-space propagation
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Phase vs. Amplitude effects with hard X-rays
Phase-contrast could be observed also when absorption-contrast undetectable
Gain up to a few 1000!
(by P. Cloetens, ESRF, France)
@ 25 keV
Absorption image Phase-contrast image
@ 10 keV
Absorption image
Images of a Mimosa flower (D. Dreossi & co.)
Phase-contrast image
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Radiographs of an AlPdMn grain recorded at the ESRF (France)
Absorption radiograph
Phase radiograph
Mancini L., PhD Thesis, 1998
Mancini L. et al., Phil. Mag. A 78 (1998) 1175
200 mm
lamellae
holes
E = 35.5 keV
~3 cm
Lezard
E = 17 keV
d = 50 cm
Courtesy of A. Astolfo SYRMEP
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Synchrotron X-ray computed microtomography (m -CT)
PC
Sample
Scintillator Screen
CCD camera
White or monochromatic X-ray beam
y
x
z
d
q
Planar Radiographs Sample Stage
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 Lens-coupled
16 bit, 2048 x 2048 pixels2
pixel size: 7.4x7.4 mm2
FOV: continuously adjustable
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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
TomoLab: a cone-beam m-CT station @Elettra
Inside the facility
X-ray
sourc
e
Flat
panel
detect
or
Sample stage
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
The ICTP-Elettra X-ray laboratory for
cultural heritage, archaeology and paleontology
Coordinator: Prof. Claudio Tuniz
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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)
Courtesy of S. Favretto
Lezard
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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
Agreement among the Public Hospital of Trieste, the University of Trieste and Elettra
Breast imaging: the SYRMA (SYnchrotron
Radiation for MAmmography) project
{Financed by Fondazione Cassa di Risparmio di Trieste}
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Phase-contrast
radiography
Tesei L. et al., Nucl. Instrum. and Meth. A, 548 (2005) 257-263
E = 29 keV, d = 17 cm
Implanted bone
Biomaterials
1 mm
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2 mm
Food science
1 mm Voxel=(8x6.78x2.8) mm3
E = 13 keV
d = 6 cm
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
Aerated chocolate Bread crumb
E = 12 keV
d = 20 cm
Polymeric foams Wood
Soft matter
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Non-destructive evaluation of ancient
musical instruments
Heat transfer in Aluminum metal foams
STL modeling and Computational Fluid Dynamics simulations
P. Ranut , E. Nobile, L. Mancini, Experimental Thermal and Fluid Science (2015)
30 PPI 20 PPI 10 PPI
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M. Galiová, J. Kaiser et al., Analytical and Bioanalytical Chemistry, 398 (2010) 1095
Paleontology
Pathological fossil snake vertebra (1 Ma. old)
1 mm
1 mm
Bee trapped in Amber 20-40 Ma. old found
in the Dominican Republic
Greco M.K. et al., Insectes Sociaux, 8 (2011) 1-8
Swiss Bee Research Centre
1 mm
E = 14 keV
d = 20 cm
# of proj. = 900
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
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N. Marinoni et al., Journal of Material Science, 44 (2009) 5815-5823.
J. Kaiser et al., Urological Research, (2010), in press.
Cement-based materials
Human kidney stones
Multi-phase systems
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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Pore3D is a tool for 3D image processing and analysis
http://www.elettra.eu/pore3d
Filters
Basic (mean, median, gaussian, ...)
Anisotropic diffusion
Bilateral
Ring artifacts reduction
Binary (median, clear border, ...)
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
Skeleton extraction
Thinning
Medial axis (LKC)
DOHT
Gradient Vector Flow
Skeleton pruning
Skeleton labeling
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
The Pore3D software library @ Elettra
S. Puce et al., Zoomorphology, 130 (2011) 85-95
3D rendering of a branch
3D analysis of the canal network of Stylaster sp.
(Cnidaria, Hydrozoa) by means of X-ray mCT
Colony in situ
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DACTYLOPORE
Section of a branch without coenostem
AMPULLAE
THIN CANALS
GASTROPORE
TomoLab
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
Old and new gastropores
surrounded by a single ring
of dactylopores
Cyclosystem Cyclosystem enlargement Cyclosystems completely
separated
Study of the growth process
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)
M.J. Blunt et al., Advances in Water Resources, 51 (2013) 197-216.
S. Iglauer et al., Fuel, 103 (2013) 905-914.
Portland limestone Indiana limestone Guilting limestone
Middle Eastern carbonates Mount Gambier limestone
Clashach sandstone: oil-water distribution
3D distribution of brine (blue) and residual oil clusters (red)
voxel size: 9 mm
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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.
Courtesy of M. Polacci (INGV, Pisa)
SYRMEP
D.R. Baker, L. Mancini et al., Lithos, 148 (2012) 262-276 Sagittal and frontal slices
pixel size = 9 μm
E = 28 keV
mCT images of a pumice rock from Ambrym volcano
@ SYRMEP
Axial view
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D.R. Baker, L. Mancini et al., Lithos, 148 (2012) 262-276
3D movie of a pumice rock from Ambrym volcano
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 %
D. Zandomeneghi et al., Geosphere, 6 (2010) 793-804
Scoria from Stromboli, poorly to moderately vesiculated, highly crystallized
Blue: pyroxene crystals
Yellow: feldspar crystals
vesicles -> 36 %
pyroxenes -> 28%
feldspars -> 12%,
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M. Voltolini et al., J. of Volc. and Geothermal Res., 202 (2011) 83-95
Scoria from Etna (experiments performed at the TOMCAT
beamline at the Swiss Synchrotron Light Source, PSI)
oxides
feldspars pyroxenes
vesicles -> 68.9%, plagioclases -> 4.3%, pyroxenes -> 3.2%, “oxides” -> 0.7%, glass -> 22.9%. vesicles -> 68.9%, plagioclases -> 4.3%, pyroxenes -> 3.2%, “oxides” -> 0.7%, glass -> 22.9%
voxel size: 1.85 μm
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
43
Synthetic trachyte sample (material from Campi Flegrei)
Reconstructed axial slice
after phase-retrieval Reconstructed axial slice
F. Arzilli, L. Mancini, et al., Lithos, 216-217 (2015) 93-105
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F. Arzilli, L. Mancini et al., Lithos, 216-217 (2015) 93-105
3D segmentation and separation of alkali-feldspar spherulites
3D visualization of a alkali-feldspar spherulite
F. Arzilli, L. Mancini et al., Lithos, 216-217 (2015) 93-105
6/22/2015
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In the Pole Figures the long,
medium and short axes of
the ellipsoids used for fitting
the single lamella are
plotted.
3D Shape Preferred Orientation (SPO) analyses
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)
Sample spindle
Laser
Microscope
and CMOS
camera
D.R. Baker et al., Nature Communications, 3 (2012) 1135
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.
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Skeletonization to measure bubble and pore throat sizes
in a volcanic rock ((3 wt.% of dissolved H2O)
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.
a) b) c)
D.R. Baker et al., Nature Communications, 3 (2012) 1135
Experiments vs. natural Bubble Size Distributions
Polacci et al., J. of Geophysical Research, 114 (2009) B01206
Normal Strombolian eruption Paroxysmal eruption
4D experiments
D.R. Baker et al., Nature
Comm., 3 (2012) 1135
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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 Sample size/
material
Beamtime
availability
Info
to extract
Sample
damage
Vi aspettiamo @ Elettra!
Grazie per l’attenzione
6/22/2015
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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
E grazie a ….
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