Poisson noise removal from high-resolution STEM images based on periodic block matching
10.1186/s40679-015-0004-8
Crossref journal-article
Springer Science and Business Media LLC
Advanced Structural and Chemical Imaging (297)
Abstract

AbstractScanning transmission electron microscopy (STEM) provides sub-ångstrom, atomic resolution images of crystalline structures. However, in many applications, the ability to extract information such as atom positions, from such electron micrographs, is severely obstructed by low signal-to-noise ratios of the acquired images resulting from necessary limitations to the electron dose. We present a denoising strategy tailored to the special features of atomic-resolution electron micrographs of crystals limited by Poisson noise based on the block-matching and 3D-filtering (BM3D) algorithm by Dabov et al. We also present an economized block-matching strategy that exploits the periodic structure of the observed crystals. On simulated single-shot STEM images of inorganic materials, with incident electron doses below 4 C/cm 2, our new method achieves precisions of 7 to 15 pm and an increase in peak signal-to-noise ratio (PSNR) of 15 to 20 dB compared to noisy images and 2 to 4 dB compared to images denoised with the original BM3D.

Bibliography

Mevenkamp, N., Binev, P., Dahmen, W., Voyles, P. M., Yankovich, A. B., & Berkels, B. (2015). Poisson noise removal from high-resolution STEM images based on periodic block matching. Advanced Structural and Chemical Imaging, 1(1).

Authors 6
  1. Niklas Mevenkamp (first)
  2. Peter Binev (additional)
  3. Wolfgang Dahmen (additional)
  4. Paul M Voyles (additional)
  5. Andrew B Yankovich (additional)
  6. Benjamin Berkels (additional)
References 33 Referenced 35
  1. Batson, PE, Dellby, N, Krivanek OL: Sub-ångstrom resolution using aberration corrected electron optics. Nature. 418(6898), 617–620 (2002). (10.1038/nature00972) / Nature by PE Batson (2002)
  2. Berkels, B, Binev, P, Blom, DA, Dahmen, W, Sharpley, R, Vogt, T: Optimized imaging using non-rigid registration. Ultramicroscopy. 138, 46–56 (2014). (10.1016/j.ultramic.2013.11.007) / Ultramicroscopy by B Berkels (2014)
  3. Ortalan, V, Uzan, A, Gates, BC, Browning, ND: Direct imaging of single metal atoms and clusters in the pores of dealuminated HY zeolite. Nat. Nanotechnol. 5, 506–510 (2010). (10.1038/nnano.2010.92) / Nat. Nanotechnol by V Ortalan (2010)
  4. Houben, L, Thust, A, Urban, K: Atomic-precision determination of the reconstruction of a 90 degree tilt boundary in YBa 2 Cu 3 O 7−δ by aberration corrected HRTEM. Ultramicroscopy. 106(3), 200–214 (2006). (10.1016/j.ultramic.2005.07.009) / Ultramicroscopy by L Houben (2006)
  5. Jia, C-L, Urban, K, Alexe, M, Hesse, D, Vrejoiu, I: Direct observation of continuous electric dipole rotation in flux-closure domains in ferroelectric Pb(Zr,Ti)O 3. Science. 331(6023), 1420–1423 (2011). (10.1126/science.1200605) / Science by C-L Jia (2011)
  6. Schmid, H, Okunishi, E, Oikawa, T, Mader, W: Structural and elemental analysis of iron and indium doped zinc oxide by spectroscopic imaging in cs-corrected. STEM Micron. 43(1), 49–56 (2012). (10.1016/j.micron.2011.05.011) / STEM Micron by H Schmid (2012)
  7. Kimoto, K, Asaka, T, Yu, X, Nagai, T, Matsui, Y, Ishizuka, K: Local crystal structure analysis with several picometer precision using scanning transmission electron microscopy. Ultramicroscopy. 110(7), 778–782 (2010). (10.1016/j.ultramic.2009.11.014) / Ultramicroscopy by K Kimoto (2010)
  8. Yankovich, AB, Berkels, B, Dahmen, W, Binev, P, Sanchez, SI, Bradley, SA, Li, A, Szlufarska, I, Voyles, PM: Picometre-precision analysis of scanning transmission electron microscopy images of platinum nanocatalysts. Nat. Commun (2014). doi:10.1038/ncomms5155. (10.1038/ncomms5155)
  9. Nellist, PD, Pennycook, SJ: Accurate structure determination from image reconstruction in adf stem. J. Microsc. 190(1-2), 159–170 (1998). (10.1046/j.1365-2818.1998.3260881.x) / J. Microsc. by PD Nellist (1998)
  10. Rosenauer, A, Mehrtensx, T, Müller, K, Gries, K, Schowalter, M, Venkata Satyam, P, Bley, S, Tessarek, C, Hommel, D, Sebald, K, Seyfried, M, Gutowski, J, Avramescu, A, Engl, K, Lutgen, S: Composition mapping in ingan by scanning transmission electron microscopy. Ultramicroscopy. 111(8), 1316–1327 (2011). (10.1016/j.ultramic.2011.04.009) / Ultramicroscopy by A Rosenauer (2011)
  11. Kim, Y-M, He, J, Biegalski, MD, Ambaye, H, Lauter, V, Christen, HM, Pantelides, ST, Pennycook, SJ, Kalinin, SV, Borisevich, AY: Probing oxygen vacancy concentration and homogeneity in solid-oxide fuel-cell cathode materials on the subunit-cell level. Nat. Mater. 11(10), 888–894 (2012). (10.1038/nmat3393) / Nat. Mater. by Y-M Kim (2012)
  12. Morgan, DG, Ramasse, QM, Browning, ND: Application of two-dimensional crystallography and image processing to atomic resolution z-contrast images. J. Electron Microsc. 58(3), 223–244 (2009). (10.1093/jmicro/dfp007) / J. Electron Microsc. by DG Morgan (2009)
  13. Unwin, PNT, Henderson, R: Molecular structure determination by electron microscopy of unstained crystalline specimens. J. Mol. Biol. 94(3), 425–440 (1975). (10.1016/0022-2836(75)90212-0) / J. Mol. Biol. by PNT Unwin (1975)
  14. Klug, A: Image analysis and reconstruction in the electron microscopy of biological macromolecules. Chemica Scripta. 14, 1978–1979.
  15. Hovmöller, S, Sjögren, A, Farrants, G, Sundberg, M, Marinder, B-O: Accurate atomic positions from electron microscopy. Nature. 311, 238–241 (1984). (10.1038/311238a0) / Nature by S Hovmöller (1984)
  16. Hovmöller, S: Crisp: crystallographic image processing on a personal computer. Ultramicroscopy. 41(1), 121–135 (1992). (10.1016/0304-3991(92)90102-P) / Ultramicroscopy by S Hovmöller (1992)
  17. Buades, A, Coll, B, Morel, J-M: A review of image denoising algorithms, with a new one. Multiscale Model. Simul. 4(2), 490–530 (2005). (10.1137/040616024) / Multiscale Model. Simul. by A Buades (2005)
  18. Binev, P, Blanco-Silva, F, Blom, D, Dahmen, W, Lamby, P, Sharpley, R, Vogt, T: Modeling Nanoscale Imaging in Electron Microscopy. Nanostructure Science and Technology. In: Vogt, T, Dahmen, W, Binev, P (eds.), pp. 127–145. Springer, New York City (2012). (10.1007/978-1-4614-2191-7_5)
  19. Wei, D-Y, Yin, C-C: An optimized locally adaptive non-local means denoising filter for cryo-electron microscopy data. J. Struct. Biol. 172(3), 211–218 (2010). (10.1016/j.jsb.2010.06.021) / J. Struct. Biol. by D-Y Wei (2010)
  20. Mevenkamp, N, Yankovich, AB, Voyles, PM, Berkels, B: Non-local means for scanning transmission electron microscopy images and poisson noise based on adaptive periodic similarity search and patch regularization. In: Bender, J, Kuijper, A, von Landesberger, T, Theisel, H, Urban, P (eds.)VMV 2014: Vision, Modeling & Visualization, pp. 63–70. Eurographics Association, Darmstadt, Germany (2014).
  21. Bergmann, R: The fast Fourier transform and fast wavelet transform for patterns on the torus. Appl. Comput. Harmonic Anal. 35(1), 39–51 (2013). (10.1016/j.acha.2012.07.007) / Appl. Comput. Harmonic Anal. by R Bergmann (2013)
  22. Coupé, P, Yger, P, Prima, S, Hellier, P, Kervrann, C, Barillot, C: An Optimized Blockwise Nonlocal Means Denoising Filter for 3-D Magnetic Resonance Images. IEEE Trans. Med. Imaging. 27(4), 425–441 (2008). (10.1109/TMI.2007.906087) / IEEE Trans. Med. Imaging by P Coupé (2008)
  23. Salmon, J, Harmany, Z, Deledalle, CA, Willett, R: Poisson noise reduction with non-local PCA. J. Math. Imaging Vis. 48(2), 279–294 (2013). (10.1007/s10851-013-0435-6) / J. Math. Imaging Vis. by J Salmon (2013)
  24. Dabov, K, Foi, A, Katkovnik, V, Egiazarian, K: Image Denoising by sparse 3-D transform-domain collaborative filtering. Image Process. IEEE Trans. 16(8), 2080–2095 (2007). (10.1109/TIP.2007.901238) / Image Process. IEEE Trans. by K Dabov (2007)
  25. Anscombe, FJ: The transformation of poisson, binomial and negative-binomial data. Biometrika Trust. 35, 246–254 (1948). (10.1093/biomet/35.3-4.246) / Biometrika Trust by FJ Anscombe (1948)
  26. Mäkitalo, M, Foi, A: Optimal inversion of the anscombe transformation in low-count poisson image denoising. Image Process. IEEE Trans. 20(1), 99–109 (2011). (10.1109/TIP.2010.2056693) / Image Process. IEEE Trans. by M Mäkitalo (2011)
  27. Deledalle, C-A, Tupin, F, Denis, L: Poisson NL means: Unsupervised non local means for Poisson noise. In: Paper presented at the 17th Internal Conference on Image Processing, pp. 801–804. IEEE, Hong Kong (26–29 September 2010). (10.1109/ICIP.2010.5653394)
  28. Dabov, K, Foi, A, Katkovnik, V, Egiazarian, K: Image denoising with block-matching and 3D filtering. Proc. SPIE. 6064, 606414–60641412 (2006). (10.1117/12.643267) / Proc. SPIE by K Dabov (2006)
  29. Maggioni, M, Sánchez-Monge, E, Foi, A, Danielyan, A, Dabov, K, Katkovnik, V, Egiazarian, K: Image and Video Denoising by Sparse 3D Transform-domain Collaborative Filtering: Block-matching and 3D Filtering (BM3D) Algorithm and Its Extensions. Tampere University of Technology, http://www.cs.tut.fi/~foi/GCF-BM3D/ Accessed date November, 10th 2014.
  30. Mäkitalo, M, Foi, A: Optimal Inversion of the Anscombe and Generalized Anscombe Variance-stabilizing Transformations. Tampere University of Technology. http://www.cs.tut.fi/~foi/invansc/ Accessed date November, 10th 2014.
  31. Martin, DC, Chen, J, Yang, J, Drummy, LF, Kübel, C: High resolution electron microscopy of ordered polymers and organic molecular crystals: Recent developments and future possibilities. J. Polymer Sci. Part B: Polymer Phys. 43(14), 1749–1778 (2005). (10.1002/polb.20419) / J. Polymer Sci. Part B: Polymer Phys. by DC Martin (2005)
  32. Kirkland, EJ: Advanced Computing in Electron Microscopy. 2nd edn. Springer, New York City (2010). (10.1007/978-1-4419-6533-2) / Advanced Computing in Electron Microscopy by EJ Kirkland (2010)
  33. Van Aert, S, Den Dekker, AJ, Van Den Bos, A, Van Dyck, D, Chen, JH: Maximum likelihood estimation of structure parameters from high resolution electron microscopy images. Part II: a practical example. Ultramicroscopy. 104(2), 107–125 (2005). (10.1016/j.ultramic.2005.03.002) / Ultramicroscopy by S Van Aert (2005)
Dates
Type When
Created 10 years, 4 months ago (March 24, 2015, 8:40 a.m.)
Deposited 4 years ago (July 30, 2021, 4:01 a.m.)
Indexed 3 months, 1 week ago (May 13, 2025, 10:03 a.m.)
Issued 10 years, 4 months ago (March 25, 2015)
Published 10 years, 4 months ago (March 25, 2015)
Published Online 10 years, 4 months ago (March 25, 2015)
Published Print 9 years, 8 months ago (Dec. 1, 2015)
Funders 0

None

@article{Mevenkamp_2015, title={Poisson noise removal from high-resolution STEM images based on periodic block matching}, volume={1}, ISSN={2198-0926}, url={http://dx.doi.org/10.1186/s40679-015-0004-8}, DOI={10.1186/s40679-015-0004-8}, number={1}, journal={Advanced Structural and Chemical Imaging}, publisher={Springer Science and Business Media LLC}, author={Mevenkamp, Niklas and Binev, Peter and Dahmen, Wolfgang and Voyles, Paul M and Yankovich, Andrew B and Berkels, Benjamin}, year={2015}, month=mar }