Towards accurate measurements with synchrotron tomography Problems and pitfalls. Robert C. Atwood. Nghia T. Vo, Michael Drakopoulos, Thomas Connolley

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1 Towards accurate measurements with synchrotron tomography Problems and pitfalls Robert C. Atwood Nghia T. Vo, Michael Drakopoulos, Thomas Connolley

2 Artefacts in Synchrotron X-ray Tomography Rings Rings Rings Zingers Beam Fluctuation Phase contrast when you don t want it Misalignment Distortion Scintillator defects (rings!) Robert C. Atwood

3 X-ray Energy Range at JEEP 50 kev 150 kev An Inch of Steel

4 I12 JEEP Component layout Filters Attenuators Wiggler Slits Large Sample Manipulator 100 [m from source] Slits 88 Sample Manipulator 57 Slits crystal Laue Monochromator Detectors 17 m Diamond filter Removes low energies Detectors Robert C. Atwood

5

6 Camera with shielding Roll stage for camera alignment Z-stage for camera focus Scintillators X-stage for module change

7 Rings, Rings, Rings Robert C. Atwood Features fixed in the image while the sample rotates -- dust -- other contamination -- scratches -- crystal defects

8 Rings, Rings, Rings Features that appear and grow DURING the scan! Robert C. Atwood

9 Sinogram of one slice 0 Theta 180 Big Particle Small Particles Horizontal Distance x Robert C. Atwood

10 Tomographic Reconstruction of one slice Big Particle Area of Interest Fossil Small Particles

11 Tomographic Reconstruction of one slice With mathematical Ring Suppression Area of Interest Fossil

12 After hours of painstaking manual tracing, ignoring the rings (and the cracks in the fossil itself) Garwood et. al. rings painful especially when manual intervention required anyway! -- Russell J. Garwood, Palaeontologist and Image Processing specialist

13 Zingers Small, often single pixel bright points Persisting for only one image Caused by X-ray photons striking the electronic detector Robert C. Atwood

14 Zingers If uncorrected, they result in straight lines in the reconstruction Robert C. Atwood

15 High Energy Imaging 130 kev 6 mm Steel Spheres Greater X-ray scatter Longer exposure required 1mm 1mm Robert C. Atwood

16 Contrast vs. Projections Image Characterization : How Many Projections? 6000 Projections 1500 Projections 300 Projections Contrast Ratio 1mm Step Contrast of the Gap between Steel Balls is decreased as expected 16

17 Energy (kev) Image Characterization Energy and Time 5 mm mm Flower, in a plastic tube Total Tomography Time (seconds)

18 B C 53 kev; 50 seconds; 6000 projections 150 kev; 500 seconds; 6000 projections

19 Robert C. Atwood Phase contrast

20 Phase contrast images Absorption Phase retrieval Polypropylene, Polyethylene and Cellulose Acetate spheres 53 kev 2200 mm, 2100 mm and 300 mm Camera Distance NT Vo, RC Atwood, PD Lee, MBH Breese, M Drakopoulos, and HO Moser, An acceleration technique for iterative phase retrieval applicable for in-line X- ray phase contrast tomography Applied Physics Letters (Under review) Robert C. Atwood

21 Phase contrast reconstruction Absorption Phase retrieval PP: Polypropylene; PE: Polyethylene; CA: Cellulose Acetate Robert C. Atwood

22 Misalignment Points expanded into circular features Obvious, in this case but.. Robert C. Atwood

23 Small differences.. Which is the better alignment? Slice Count Total Area Average Size %Area Mean Feret FeretX FeretY MinFeret E E E

24 Impossible misalignment?

25 Distortion Due to requirments of Radiation-Hard Lenses CoD CoR COD: Centre of Distortion COR: Centre of Rotation This object is a sphere

26 Distortion correction at sub-pixel accuracy NIST traceable microscope calibration grid Mapping formula (backward) r d = k 2 3 n 0 + k 1 r u +k 2 r u + k 3 r u +...k n r u ru Must be Updated after any adjustment of the optics! Polynomial coefficents are unlikely to change but the centre of distortion can easily change when mirrors or lenses are disturbed for cleaning Using Vo s method[*] to calculate these coefficients [*] Nghia T. Vo, Robert C. Atwood, and Michael Drakopoulos, "Radial lens distortion correction with sub-pixel accuracy for X-ray microtomography," Opt. Express 23, (2015). 26

27 Distortion correction at sub-pixel accuracy 1 2 Spherical object is recovered. Small bubbles were smeared by distortion and are reconstructed properly. 27

28 Scintillator 032 after repeated cleaning and use Trying to remove the needle-like crystals resulted in white residue despite residue free filtered solvents as well as the possibility of introducing scratches

29 Scintillator after use Some features appear and grow during exposure to X-rays. Reactive species, ablation and electrostatic charging are contributing. Cleaning sometimes removes these but leaves other residue..

30 Scintillators as-received (Dark field visible light) 0.2 mm High density of small bright points. They appear to be aligned as roughly equally spaced lines. We could not at present determine if they are deposits or defects i.e. bumps or pits. They may be droplets of polishing residue (oil) Robert C. Atwood

31 70 micron thick crystal Lesser density of bright points, a few scratches, but some prominent parallel streaks. These are definitely associated with the crystal, they move when the crystal is moved. This could be streaks of a residue of polishing or variation in the crystal doping Robert C. Atwood 0.2 mm

32 As received scintillator 056 (X-ray) The crystal material appears to be good, however, this supplier has not been able to supply sufficiently polished surfaces. Robert C. Atwood

33 As received scintillator 057 (X-ray) If we can obtain polishing and cleaning for this material we believe we would have good scintillators Robert C. Atwood

34 B16 X-ray tests With Steel Sample partly in beam Scintillator defects scatter the light in the dark region mm 0. 5mm thickness Without sample Bright features are scintillator defects Dark features are monochromator defects) Broad bands are??bending fringes?? Robert C. Atwood

35 Robert C. Atwood HELP!

36 Acknowledgements Co authors Nghia T. Vo, Thomas Connolley, Michael Drakopoulos Oxana Magdysyuk for work with scintillators Russell J. Garwood (U. Manchester) for Spider Fossil problems Technical support at Diamond; Bob Humphreys, Tom Cobb, Paul Roberts, Nicoletta Di Maio, Jon Thompson Robert C. Atwood 36

37 Robert C. Atwood

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