Self-adapting denoising, alignment and reconstruction in electron tomography in materials science

Ultramicroscopy

Volumn 160, Issue , 2016, Pages 23-34

  Printemps, Tony ^a,b   Mula, Guido ^c   Sette, Daniele ^a,b   Bleuet, Pierre ^a,b   Delaye, Vincent ^a,b   Bernier, Nicolas ^a,b   Grenier, Adeline ^a,b   Audoit, Guillaume ^a,b   Gambacorti, Narciso ^a,b   Hervé, Lionel ^a,b  

^a UNIV GRENOBLE ALPES   (France)

^b CEA GRENOBLE   (France)

^c UNIVERSITY OF CAGLIARI   (Italy)

Author keywords

Denoising; Electron tomography; IBF; Porous silicon; Silver nanoparticles; Wavelet

Indexed keywords

DATA ACQUISITION; ELECTRONS; GAUSSIAN NOISE (ELECTRONIC); IMAGE RECONSTRUCTION; METAL NANOPARTICLES; MIXING; NANOPARTICLES; POROUS SILICON; REPAIR; SILVER; TOMOGRAPHY; WAVELET TRANSFORMS;

DE-NOISING; ELECTRON TOMOGRAPHY; IBF; SILVER NANOPARTICLES; WAVELET;

ELECTRIC IMPEDANCE TOMOGRAPHY;

SILICON; SILVER NANOPARTICLE;

ACCURACY; ALGORITHM; ARTICLE; ARTIFACT; AUTOMATION; ELECTRON TOMOGRAPHY; INFORMATION PROCESSING; MATERIAL SCIENCE; MATHEMATICAL ANALYSIS; NOISE; PHYSICAL PHENOMENA; POROSITY; RELIABILITY; SCIENCE; SELF-ADAPTING DENOISING ALIGNMENT AND RECONSTRUCTION; SIMULATION; THREE DIMENSIONAL IMAGING; WAVELET ANALYSIS;

EID: 84942342643     PISSN: 03043991     EISSN: 18792723     Source Type: Journal    
DOI: 10.1016/j.ultramic.2015.09.007     Document Type: Article

References (42)

1. Midgley P.A., Weyland M. 3D electron microscopy in the physical sciences: the development of Z-contrast and EFTEM tomography. Ultramicroscopy 2003, 96(3-4):413-431.
2. Cardone G., Grünewald K., Steven A.C. A resolution criterion for electron tomography based on cross-validation. J. Struct. Biol. 2005, 151(2):117-129.
3. Heidari Mezerji H., Van den Broek W., Bals S. A practical method to determine the effective resolution in incoherent experimental electron tomography. Ultramicroscopy Apr. 2011, 111(5):330-336.
4. Gilbert P. Iterative methods for the three-dimensional reconstruction of an object from projections. J. Theor. Biol. 1972, 36(1):105-117.
5. van Aarle W., Batenburg K.J., Van Gompel G., Van de Casteele E., Sijbers J. Super-resolution for computed tomography based on discrete tomography. IEEE Trans. Image Process. 2014, 23(3):1181-1193.
6. Leary R., Saghi Z., Midgley P.A., Holland D. Compressed sensing electron tomography. Ultramicroscopy 2013, 131:70-91.
7. Goris B., Roelandts T., Batenburg K.J., Heidari Mezerji H., Bals S. Advanced reconstruction algorithms for electron tomography: from comparison to combination. Ultramicroscopy 2013, 127:40-47.
8. Goris B., Van den Broek W., Batenburg K.J., Heidari Mezerji H., Bals S. Electron tomography based on a total variation minimization reconstruction technique. Ultramicroscopy 2012, 113:120-130.
9. Altantzis T., Goris B., Sánchez-Iglesias A., Grzelczak M., Liz-Marzán L.M., Bals S. Quantitative structure determination of large three-dimensional nanoparticle assemblies. Part. Part. Syst. Charact. 2013, 30(1):84-88.
10. Li C., Yin W., Jiang H., Zhang Y. An efficient augmented Lagrangian method with applications to total variation minimization. Comput. Optim. Appl. 2013, 56(3):507-530.
11. Uhlir A., Uhlir I. Historical perspective on the discovery of porous silicon. Phys. Status Solidi C: Conf. 2005, 2:3185-3187.
12. Uhlir A. Electrolytic shaping of germanium and silicon. Bell Syst. Tech. J 1956, 35:333-347.
13. Bisi O., Ossicini S., Pavesi L. Porous silicon: a quantum sponge structure for silicon based optoelectronics. Surf. Sci. Rep. 2000, 38:1-126.
14. Suárez I., Chirvony V., Hill D., Martínez-Pastor J. Simulation of surface-modified porous silicon photonic crystals for biosensing applications. Photonics Nanostruct.-Fundam. Appl 2012, 10(3):304-311.
15. Leacock-Johnson A., Garcia Sega A., Sharief A., Sailor M.J., Miskelly G.M. Real-time 1D hyperspectral imaging of porous silicon-based photonic crystals with one-dimensional chemical composition gradients undergoing pore-filling-induced spectral shifts. Sens. Actuators A Phys. 2013, 203:154-159.
16. McInnes S.J.P., Voelcker N.H. Porous Silicon for Biomedical Applications 2014.
17. Sailor M.J. Porous Silicon in Practice: Preparation, Characterization and Applications 2012.
18. Bleuet P., Audoit G., Barnes J.-P., Bertheau J., Dabin Y., Dansas H., Fabbri J.-M., Florin B., Gergaud P., Grenier A., Haberfehlner G., Lay E., Laurencin J., Serra R., Villanova J. Specifications for Hard Condensed Matter Specimens for Three-Dimensional High-Resolution Tomographies. Microsc. Microanal. 2013, 19(03):726-739.
19. V. Subramanian, J.B. Chang, A.D.L.F. Vornbrock, D.C. Huang, L. Jagannathan, F. Liao, B. Mattis, S. Molesa, D.R. Redinger, D. Soltman, S.K. Volkman, Q. Zhang, Printed electronics for low-cost electronic systems: technology status and application development, in: Proceedings of the ESSDERC 2008 - 38th European Solid-State Device Research Conference, 2008. pp. 17-24.
20. Eom S.H., Senthilarasu S., Uthirakumar P., Hong C.-H., Lee Y.-S., Lim J., Yoon S.C., Lee C., Lee S.-H. Preparation and characterization of nano-scale ZnO as a buffer layer for inkjet printing of silver cathode in polymer solar cells. Sol. Energy Mater. Sol. Cells 2008, 92(5):564-570.
21. Fuller S.B., Wilhelm E.J., Jacobson J.M. Ink-jet printed nanoparticle microelectromechanical systems. J. Microelectromech. Syst. 2002, 11(1):54-60.
22. D. Sette, D. Mercier, P. Brunet-Manquat, C. Poulain, A. Blayo, Micro Pirani pressure sensor fabricated by inkjet printing of silver nanoparticles in: Proceedings of the Solid-State Sensors, Actuators and Microsystems (Transducers & Eurosensors XXVII), June, 2013, pp. 1783-1786.
23. D. Sette, A. Blayo, Silver nanoparticle inkjet printed 17GHz filter, in: Proceedings of the Microwave Symposium Digest (IMS), 2013 IEEE MTT-S International, 2013, pp. 1-4.
24. Park M., Im J., Shin M., Min Y., Park J., Cho H., Park S., Shim M.-B., Jeon S., Chung D.-Y., Bae J., Park J., Jeong U., Kim K. Highly stretchable electric circuits from a composite material of silver nanoparticles and elastomeric fibres. Nat. Nanotechnol. 2012, 7(12):803-809.
25. Ercius P., Muller D. Incoherent bright field STEM for imaging and tomography of ultra-thick TEM cross-sections. Microsc. Microanal. 2009, 15(Suppl. 2):S238-S239.
26. Starck J.-L., Fadili J., Murtagh F. The undecimated wavelet decomposition and its reconstruction. IEEE Trans. Image Process. 2007, 16(2):297-309.
27. De Siqueira A.F., Cabrera F.C., Pagamisse A., Job A.E. Segmentation of scanning electron microscopy images from natural rubber samples with gold nanoparticles using starlet wavelets. Microsc. Res. Tech. 2014, 77(1):71-78.
28. Anscombe F. The transformation of Poisson, binomial and negative-binomial data,. Biometrika 1948, 246-254.
29. Murtagh F., Starck J.-L., Bijaoui a Image restoration with noise suppression using a multiresolution support. Astron. Astrophys. Suppl. 1995, 112:179.
30. Starck J.-L., Bobin J. Astronomical data analysis and sparsity: from wavelets to compressed sensing. Proc. IEEE 2010, 98(6):1021-1030.
31. Starck J., Murtagh F., Fadili J. Sparse Image and Signal Processing: Wavelets, Curvelets, Morphological Diversity 2010, Cambridge University Press, New York, USA.
32. Starck J.-L., Candès E.J., Donoho D.L. The curvelet transform for image denoising. IEEE Trans. Image Process 2002, 11(6):670-684.
33. Donoho D.L., Johnstone J.M. Ideal spatial adaptation by wavelet shrinkage. Biometrika 1994, 81(3):425-455.
34. Liu Y., Penczek P.A., McEwen B.F., Franks J. A marker-free alignment method for electron tomography. Ultramicroscopy 1995, 58(3-4):393-402.
35. M. Cop, J. Dengler, A multi-resolution approach to the 3D reconstruction of a 50s ribosome from an EM-Tilt Series solving the alignment problem without gold particles, in: Proceedings of the 10th International Conference Pattern Recognition, 1990.
36. Houben L., Sadan M.Bar Refinement procedure for the image alignment in high-resolution electron tomography. Ultramicroscopy 2011, 111(9-10):1512-1520.
37. Dax A. Line search acceleration of iterative methods. Linear Algebra Appl. 1990, 130:43-63.
38. Palenstijn W.J., Batenburg K.J., Sijbers J. Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs). J. Struct. Biol. 2011, 176(2):250-253.
39. Otsu N. A Tlreshold Selection Method from Gray-Level Histograms. Syst. Man Cybern. IEEE Trans. 1979, 9(1):62-66.
40. Serra J. Introduction to mathematical morphology. Comput. Vis. Graph. Image Process 1986, 35(3):283-305.
41. Stoschek A., Hegerl R. Denoising of electron tomographic reconstructions using multiscale transformations. J. Struct. Biol. 1997, 120(3):257-265.
42. Maiorca M., Hanssen E., Kazmierczak E., Maco B., Kudryashev M., Hall R., Quiney H., Tilley L. Improving the quality of electron tomography image volumes using pre-reconstruction filtering. J. Struct. Biol. 2012, 180(1):132-142.