Skip to main content Accessibility help

Suppressing Electron Exposure Artifacts: An Electron Scanning Paradigm with Bayesian Machine Learning

  • Karl Hujsak (a1), Benjamin D. Myers (a1) (a2), Eric Roth (a1) (a2), Yue Li (a3) and Vinayak P. Dravid (a1) (a2) (a3)...


Electron microscopy of biological, polymeric, and other beam-sensitive structures is often hampered by deleterious electron beam interactions. In fact, imaging of such beam-sensitive materials is limited by the allowable radiation dosage rather that capabilities of the microscope itself, which has been compounded by the availability of high brightness electron sources. Reducing dwell times to overcome dose-related artifacts, such as radiolysis and electrostatic charging, is challenging due to the inherently low contrast in imaging of many such materials. These challenges are particularly exacerbated during dynamic time-resolved, fluidic cell imaging, or three-dimensional tomographic reconstruction—all of which undergo additional dosage. Thus, there is a pressing need for the development of techniques to produce high-quality images at ever lower electron doses. In this contribution, we demonstrate direct dose reduction and suppression of beam-induced artifacts through under-sampling pixels, by as much as 80% reduction in dosage, using a commercial scanning electron microscope with an electrostatic beam blanker and a dictionary learning in-painting algorithm. This allows for multiple sparse recoverable images to be acquired at the cost of one fully sampled image. We believe this approach may open new ways to conduct imaging, which otherwise require compromising beam current and/or exposure conditions.


Corresponding author

* Corresponding author.


Hide All
Anderson, H.S., Ilic-Helms, J., Rohrer, B., Wheeler, J. & Larson, K. (2013). Sparse imaging for fast electron microscopy. In IS&T/SPIE Electronic Imaging, International Society for Optics and Photonics, Burlingame, California, USA, February 3, 2013, pp. 86570C–86512.
Baraniuk, R.G. (2007). Compressive sensing. IEEE Signal Process Mag 24(4), 118124.
Binev, P., Dahmen, W., DeVore, R., Lamby, P., Savu, D. & Sharpley, R. (2012). Compressed Sensing and Electron Microscopy. New York Dordrecht Heidelberg London: Springer.
Boudaïffa, B., Cloutier, P., Hunting, D., Huels, M.A. & Sanche, L. (2000). Resonant formation of DNA strand breaks by low-energy (3 to 20 eV) electrons. Science 287(5458), 16581660.
Bursill, L., Thomas, J. & Rao, K.-J. (1981). Stability of zeolites under electron irradiation and imaging of heavy cations in silicates. Nature 289(5794), 157158.
Candes, E. & Romberg, J. (2007). Sparsity and incoherence in compressive sampling. Inverse Probl 23(3), 969.
Candès, E.J., Romberg, J. & Tao, T. (2006). Robust uncertainty principles: Exact signal reconstruction from highly incomplete frequency information. IEEE Trans Inf Theory 52(2), 489509.
Coates, I.A. & Smith, D.K. (2010). Hierarchical assembly—dynamic gel–nanoparticle hybrid soft materials based on biologically derived building blocks. J Mater Chem 20(32), 66966702.
Cosslett, V. (1978). Radiation damage in the high resolution electron microscopy of biological materials: A review. J Microsc 113(2), 113129.
d’Alfonso, A., Freitag, B., Klenov, D. & Allen, L. (2010). Atomic-resolution chemical mapping using energy-dispersive x-ray spectroscopy. Phys Rev B 81(10), 100101.
de Jonge, N., Peckys, D.B., Kremers, G. & Piston, D. (2009). Electron microscopy of whole cells in liquid with nanometer resolution. Proc Natl Acad Sci 106(7), 21592164.
de Jonge, N. & Ross, F.M. (2011). Electron microscopy of specimens in liquid. Nat Nanotechnol 6(11), 695704.
Donoho, D.L. (2006). Compressed sensing. IEEE Trans Inf Theory 52(4), 12891306.
Duarte, M.F., Davenport, M.A., Takhar, D., Laska, J.N., Sun, T., Kelly, K.E. & Baraniuk, R.G. (2008). Single-pixel imaging via compressive sampling. IEEE Signal Process Mag 25(2), 83.
Egerton, R., Li, P. & Malac, M. (2004). Radiation damage in the TEM and SEM. Micron 35(6), 399409.
Glaeser, R.M. & Taylor, K.A. (1978). Radiation damage relative to transmission electron microscopy of biological specimens at low temperature: A review. J Microsc 112(1), 127138.
Hofmann, S., Sharma, R., Ducati, C., Du, G., Mattevi, C., Cepek, C., Cantoro, M., Pisana, S., Parvez, A. & Cervantes-Sodi, F. (2007). In situ observations of catalyst dynamics during surface-bound carbon nanotube nucleation. Nano Lett 7(3), 602608.
Isaacson, M., Johnson, D. & Crewe, A. (1973). Electron beam excitation and damage of biological molecules; its implications for specimen damage in electron microscopy. Radiat Res 55(2), 205224.
Kimoto, K., Asaka, T., Nagai, T., Saito, M., Matsui, Y. & Ishizuka, K. (2007). Element-selective imaging of atomic columns in a crystal using STEM and EELS. Nature 450(7170), 702704.
Kotakoski, J., Jin, C., Lehtinen, O., Suenaga, K. & Krasheninnikov, A. (2010). Electron knock-on damage in hexagonal boron nitride monolayers. Phys Rev B 82(11), 113404.
Li, W.-J., Mauck, R.L., Cooper, J.A., Yuan, X. & Tuan, R.S. (2007). Engineering controllable anisotropy in electrospun biodegradable nanofibrous scaffolds for musculoskeletal tissue engineering. J Biomech 40(8), 16861693.
Liu, Y., Lin, X.-M., Sun, Y. & Rajh, T. (2013). In situ visualization of self-assembly of charged gold nanoparticles. J Am Chem Soc 135(10), 37643767.
Luttun, A., Tjwa, M., Moons, L., Wu, Y., Angelillo-Scherrer, A., Liao, F., Nagy, J.A., Hooper, A., Priller, J. & De Klerck, B. (2002). Revascularization of ischemic tissues by PlGF treatment, and inhibition of tumor angiogenesis, arthritis and atherosclerosis by anti-Flt1. Nat Med 8(8), 831840.
Park, S.Y., Lytton-Jean, A.K., Lee, B., Weigand, S., Schatz, G.C. & Mirkin, C.A. (2008). DNA-programmable nanoparticle crystallization. Nature 451(7178), 553556.
Saghi, Z., Benning, M., Leary, R., Macias-Montero, M., Borras, A. & Midgley, P.A. (2015). Reduced-dose and high-speed acquisition strategies for multi-dimensional electron microscopy. Adv Struct Chem Imaging 1(1), 110.
Shih, T.K., Chang, R.-C., Lu, L.-C., Ko, W.-C. & Wang, C.-C. (2004). Adaptive digital image inpainting. In 18th International Conference on Advanced Information Networking and Applications, AINA 2004., IEEE, Fukuoka, Japan, March 30, 2004, pp. 71–76.
Stanciu, S.G., Hristu, R. & Stanciu, G.A. (2011). Digital image inpainting and microscopy imaging. Microsc Res Tech 74(11), 10491057.
Stevens, A., Yang, H., Carin, L., Arslan, I. & Browning, N.D. (2014). The potential for Bayesian compressive sensing to significantly reduce electron dose in high-resolution STEM images. Microscopy 63(1), 4151.
Talmon, Y. (1996). Transmission electron microscopy of complex fluids: The state of the art. Ber Bunsenges Phys Chem 100(3), 364372.
Teweldebrhan, D. & Balandin, A. (2009). Modification of graphene properties due to electron-beam irradiation. Appl Phys Lett 94(1), 013101.
Wang, Z., Bovik, A.C., Sheikh, H.R. & Simoncelli, E.P. (2004). Image quality assessment: From error visibility to structural similarity. IEEE Trans Image Process 13(4), 600612.
Williams, J., Elliman, R., Brown, W. & Seidel, T. (1985). Dominant influence of beam-induced interface rearrangement on solid-phase epitaxial crystallization of amorphous silicon. Phys Rev Lett 55(14), 1482.
Woehl, T.J., Jungjohann, K.L., Evans, J.E., Arslan, I., Ristenpart, W.D. & Browning, N.D. (2013). Experimental procedures to mitigate electron beam induced artifacts during in situ fluid imaging of nanomaterials. Ultramicroscopy 127, 5363.
Yuk, J.M., Park, J., Ercius, P., Kim, K., Hellebusch, D.J., Crommie, M.F., Lee, J.Y., Zettl, A. & Alivisatos, A.P. (2012). High-resolution EM of colloidal nanocrystal growth using graphene liquid cells. Science 336(6077), 6164.
Zhou, M., Chen, H., Paisley, J., Ren, L., Li, L., Xing, Z., Dunson, D., Sapiro, G. & Carin, L. (2012). Nonparametric Bayesian dictionary learning for analysis of noisy and incomplete images. IEEE Trans Image Process 21(1), 130144.
Zhou, M., Chen, H., Ren, L., Sapiro, G., Carin, L. & Paisley, J.W. (2009). Non-parametric Bayesian dictionary learning for sparse image representations. In Advances in Neural Information Processing Systems, Vancouver, Canada, December 7, 2010, pp. 2295–2303.



Altmetric attention score

Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed