Tecniche di imaging con luce di sincrotrone per lo studio dei geomateriali: dalla radiografia alla tomografia computerizzata a 4 dimensioni

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. 1

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 2

The SYRMEP beamline layout air slits i o n i z a t i o n c h a m b e r Elettra b e n d i n g m a g n e t v a c u u m s l i ts double Si(111) monochromator s a m p l e stage 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 * 10 8 phot./mm 2 s (@ 2.4 GeV, 180 ma) Source-to-sample distance: D 23 m detector Why hard X-ray imaging at a 3 rd 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 3

Absorption and Phase-Contrast radiography Synchrotron source D n = 1 - - i : refraction index sample detector d 0 Absorption contrast: due to differences in absorption of X rays in the object Refractive index: n = 1 - i d detector d 0.1 1 m Fresnel diffraction Phase contrast: due to refraction of X-rays in the object (P. Cloetens, ESRF France) Free-space propagation PC Regimes 4

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 5

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 6

Synchrotron X-ray computed microtomography (m -CT) Sample Scintillator Screen CCD camera PC y d q White or monochromatic X-ray beam x z 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 pixels 2 pixel size: (3.85) 14 x (3.85) 14 mm 2 FOV: (8) 28 mm x (8) 28 mm Photonic Science VHR 12 bit, 4008 x 2672 pixels 2 effective pixel size: 4.5x4.5 mm 2 FOV: 18 mm x 12 mm Photonic Science Lenscoupled 16 bit, 2048 x 2048 pixels 2 pixel size: 7.4x7.4 mm 2 FOV: continuously adjustable 7

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, P max = 39 W, focal spot min = 5 mm CCD camera: 12bit, pixel size = 12.5 µm, FOV ma = 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, P max = 75 W, focal spot min = 5 mm Detector: 12bit, pixel size = 50 µm, FOV ma = 120 mm x 120 mm C. Tuniz et al., NIM A, 711 (2013) 106-110 8

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 9

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 10

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 11

Food science E = 12 kev d = 20 cm Bread crumb E = 13 kev d = 6 cm Aerated chocolate 2 mm 1 mm Voxel=(8x6.78x2.8) mm 3 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 12

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) 13

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 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 Greco M.K. et al., Insectes Sociaux, 8 (2011) 1-8 14

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. 15

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,...) 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,...) http://www.elettra.eu/pore3d 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 16

Section of a branch without coenostem AMPULLAE DACTYLOPORE 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 17

m-ct imaging of multiphase flow in carbonates (core 5 mm) Portland limestone Indiana limestone Guilting limestone Middle Eastern carbonates 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) 18

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 Sagittal and frontal slices @ SYRMEP pixel size = 9 μm E = 28 kev D.R. Baker, L. Mancini et al., Lithos, 148 (2012) 262-276 19

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 20

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%. 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. 21

The phase-retrieval approach Phase retrieval Back projection Computed tomography reconstruction 43 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 22

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 23

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 24

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.% H 2 O 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 25

Skeletonization to measure bubble and pore throat sizes in a volcanic rock ((3 wt.% of dissolved H 2 O) 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 26

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! 27

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 28