Jun 23, 2017 - facilities: review and new developments. Nghia Vo. I12 â JEEP, Diamond Light Source. 1. Imaging Data Analysis at Diamond workshop, 23th ...
Data processing methods for tomographic data at synchrotron facilities: review and new developments
Nghia Vo I12 – JEEP, Diamond Light Source Imaging Data Analysis at Diamond workshop, 23th June 2017 1
What is tomography? Its projections
Sample
X-rays
Computed reconstruction
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Synchrotron-based tomography
Recording process
Reconstruction
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Basic pipeline of processing tomographic data Pre-processing Flat-field correction
Sinogram generation
Flat field
Stripe artifacts removal
Phase contrast filter
Reconstruction
Projection
Sinogram Reconstructed slice
Flat field correction
Tomopy: X-TRACT: SYMREP: UFO: PyHST: PITRE: Savu:
APS Australian Synchrotron Electra KIT ESRF INFN Diamond Light Source 4
Sources of problems - Bigger than the field of view - Keep changing during scan - Too weak or too strong absorption - Crystalline
4. Sample
1. X-ray source
3. Detector 2. Sample stage
- Fluctuating - Partially coherent - Divergent - Low flux
- Mechanical errors - Wobbling - Slow - Misaligned - Not fixed CoR
- Distortion - Non-linear effect - Point spread function - Limited field of view - Defective regions - Low dynamic range - Low frame rate - Noisy
5.Computing system
Limited resources (Memory, Speed, GPU) 5
Aims 1. Pre-processing
Projection space
Sinogram space
Image registration Stripe removal Phase retrieval Distortion correction Image filtering
2. Reconstruction
3. Post-processing
Reconstruction space Image reconstruction Ring removal
Image segmentation Object recognition
Image processing
Gold standards (for reconstructed data): - Clean, no arterfacts. - Accurate information about absorption coefficients or refractive indexes 6
1. Problems from X-ray source: fluctuating intensity
Add to the pipeline: Intensity normalization -> 1
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2. Problems from the sample stage: mechanical errors
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2. Problems from the sample stage: mechanical errors
No correction
Vertical translation correction
Horizontal translation correction
Add to the pipeline: Alignment -> 2
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2. Problems from the sample stage: centre of rotation
Use the sum of coefficients outside the double-wedge area in the Fourier space of sinogram
Available in: - Savu - Tomopy - SYRMEP
Add to the pipeline: Centre of rotation determination -> 3
[*] Nghia T. Vo, Michael Drakopoulos, Robert C. Atwood, and Christina Reinhard, "Reliable method for calculating the center of rotation in parallel-beam tomography," Opt. Express 22, 1907819086 (2014)
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3. Problems from detectors: lens distortion
ru = k0 + k1r d +k2 rd2 + k3 rd3 + ...kn rdn rd Mapping formula
Reconstructed images before and after correction [*] Nghia T. Vo, Robert C. Atwood, and Michael Drakopoulos, "Radial lens distortion correction with sub-pixel accuracy for X-ray micro-tomography," Opt. Express 23, 32859-32868 (2015).
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3. Problems from detectors: lens distortion
Add to the pipeline: Distortion correction -> 4
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3. Problems from detectors: defective regions
Flat field
Big ring artifact
Add to the pipeline: Blob removal -> 5
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4. Problems from samples: low contrast
Absorption function
Phase contrast imaging Add to the pipeline: Phase retrieval -> 6
Phase shift
ESRF data * Nghia T. Vo, Robert C. Atwood, Herbert O. Moser, Peter D. Lee, Mark B. H. Breese, and Michael Drakopoulos, “A fast-converging iterative method for X-ray in-line phase contrast tomography”, Appl. Phys. Lett 101, 224108 (2012).
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Implementation of various scanning techniques at I12-JEEP: 1 - 3600 double field-of-view technique 2 – Helical continuous scan 3 - Time series scan 4 - High speed scan 5 - Limited angle scan 6- Back-and-forward time series scan
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3600 double field-of-view technique
Add to the pipeline: Convert 360-sinogram to 180-sinogram -> 7
Helical fly scan
30 mm
FoV: 12 mm
Add to the pipeline: Convert to circular scan -> 8
Olivine sample
Time series scan
400 volumes for one experiment. One file ~ 1.67TB
High speed scan (sub-second tomography)
0.3s tomography
Add to the pipeline: cine file converter -> 9
Limited angle scan
Add to the pipeline: sinogram interpolation -> 10
Tomographic projections are reconstructed into 2D slices by using I12-JEEP in-house python codes: https://confluence.diamond.ac.uk/display/I12Tech/Reconstruction+scripts+for+time+series+tomography
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Acknowledgements + I12-JEEP staffs + Marie-Christine Zdora, Andrew Bodey, Sally Irvine, Ramona Duman – I13, I23- DLS + Wolfgang Ludwig - ESRF + Azeem Mohammed, Biao Cai, Peter Lee – MXIF, University of Manchester + Kate Dobson, Durham University + Matthew Pankhurst - University of Leeds
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