Skip to main content
    • Aa
    • Aa
  • Get access
    Check if you have access via personal or institutional login
  • Cited by 17
  • Cited by
    This article has been cited by the following publications. This list is generated based on data provided by CrossRef.

    Wang, Fang Sun, Ying Cao, Meng and Nishi, Ryuji 2016. The influence of structure depth on image blurring of micrometres-thick specimens in MeV transmission electron imaging. Micron, Vol. 83, p. 54.

    Woehl, Taylor and Keller, Robert 2016. Dark-field image contrast in transmission scanning electron microscopy: Effects of substrate thickness and detector collection angle. Ultramicroscopy, Vol. 171, p. 166.

    García-Negrete, C. A. Jiménez de Haro, M. C. Blasco, J. Soto, M. and Fernández, A. 2015. STEM-in-SEM high resolution imaging of gold nanoparticles and bivalve tissues in bioaccumulation experiments. The Analyst, Vol. 140, Issue. 9, p. 3082.

    Van Eyndhoven, G. Kurttepeli, M. Van Oers, C.J. Cool, P. Bals, S. Batenburg, K.J. and Sijbers, J. 2015. Pore REconstruction and Segmentation (PORES) method for improved porosity quantification of nanoporous materials. Ultramicroscopy, Vol. 148, p. 10.

    de Jonge, Niels Pfaff, Marina and Peckys, Diana B. 2014.

    Peckys, Diana B. and de Jonge, Niels 2014. Liquid Scanning Transmission Electron Microscopy: Imaging Protein Complexes in their Native Environment in Whole Eukaryotic Cells. Microscopy and Microanalysis, Vol. 20, Issue. 02, p. 346.

    Schuh, Tobias and de Jonge, Niels 2014. Liquid scanning transmission electron microscopy: Nanoscale imaging in micrometers-thick liquids. Comptes Rendus Physique, Vol. 15, Issue. 2-3, p. 214.

    Brodusch, Nicolas Demers, Hendrix and Gauvin, Raynald 2013. Dark-Field Imaging of Thin Specimens with a Forescatter Electron Detector at Low Accelerating Voltage. Microscopy and Microanalysis, Vol. 19, Issue. 06, p. 1688.

    Casadei, Alberto Schwender, Jil Russo-Averchi, Eleonora Rüffer, Daniel Heiss, Martin Alarcó-Lladó, Esther Jabeen, Fauzia Ramezani, Mohammad Nielsch, Kornelius and Morral, Anna Fontcuberta i 2013. Electrical transport in C-doped GaAs nanowires: surface effects. physica status solidi (RRL) - Rapid Research Letters, Vol. 7, Issue. 10, p. 890.

    Ramachandra, Ranjan Demers, Hendrix and de Jonge, Niels 2013. The Influence of the Sample Thickness on the Lateral and Axial Resolution of Aberration-Corrected Scanning Transmission Electron Microscopy. Microscopy and Microanalysis, Vol. 19, Issue. 01, p. 93.

    Welch, David A. Faller, Roland Evans, James E. and Browning, Nigel D. 2013. Simulating realistic imaging conditions for in situ liquid microscopy. Ultramicroscopy, Vol. 135, p. 36.

    Demers, Hendrix Ramachandra, Ranjan Drouin, Dominique and de Jonge, Niels 2012. The Probe Profile and Lateral Resolution of Scanning Transmission Electron Microscopy of Thick Specimens. Microscopy and Microanalysis, Vol. 18, Issue. 03, p. 582.

    de Jonge, Niels and Ross, Frances M. 2011. Electron microscopy of specimens in liquid. Nature Nanotechnology, Vol. 6, Issue. 11, p. 695.

    Demers, Hendrix Poirier-Demers, Nicolas Couture, Alexandre Réal Joly, Dany Guilmain, Marc de Jonge, Niels and Drouin, Dominique 2011. Three-dimensional electron microscopy simulation with the CASINO Monte Carlo software. Scanning, Vol. 33, Issue. 3, p. 135.

    Peckys, Diana B. Mazur, Peter Gould, Kathleen L. and de Jonge, Niels 2011. Fully Hydrated Yeast Cells Imaged with Electron Microscopy. Biophysical Journal, Vol. 100, Issue. 10, p. 2522.

    Ramachandra, Ranjan Demers, Hendrix and de Jonge, Niels 2011. Atomic-resolution scanning transmission electron microscopy through 50-nm-thick silicon nitride membranes. Applied Physics Letters, Vol. 98, Issue. 9, p. 093109.

    Wang, F. Zhang, H.-B. Cao, M. Nishi, R. and Takaoka, A. 2011. Image blurring of thick specimens due to MeV transmission electron scattering: a Monte Carlo study. Microscopy, Vol. 60, Issue. 5, p. 315.


Simulating STEM Imaging of Nanoparticles in Micrometers-Thick Substrates

  • H. Demers (a1), N. Poirier-Demers (a1), D. Drouin (a1) and N. de Jonge (a2)
  • DOI:
  • Published online: 20 October 2010

Scanning transmission electron microscope (STEM) images of three-dimensional (3D) samples were simulated. The samples consisted of a micrometer(s)-thick substrate and gold nanoparticles at various vertical positions. The atomic number (Z) contrast as obtained via the annular dark-field detector was generated. The simulations were carried out using the Monte Carlo method in the CASINO software (freeware). The software was adapted to include the STEM imaging modality, including the noise characteristics of the electron source, the conical shape of the beam, and 3D scanning. Simulated STEM images of nanoparticles on a carbon substrate revealed the influence of the electron dose on the visibility of the nanoparticles. The 3D datasets obtained by simulating focal series showed the effect of beam broadening on the spatial resolution and on the signal-to-noise ratio. Monte Carlo simulations of STEM imaging of nanoparticles on a thick water layer were compared with experimental data by programming the exact sample geometry. The simulated image corresponded to the experimental image, and the signal-to-noise levels were similar. The Monte Carlo simulation strategy described here can be used to calculate STEM images of objects of an arbitrary geometry and amorphous sample composition. This information can then be used, for example, to optimize the microscope settings for imaging sessions where a low electron dose is crucial for the design of equipment, or for the analysis of the composition of a certain specimen.

Corresponding author
Corresponding author. E-mail:
Linked references
Hide All

This list contains references from the content that can be linked to their source. For a full set of references and notes please see the PDF or HTML where available.

K. Aoyama , T. Takagi , A. Hirase & A. Miyazawa (2008). STEM tomography for thick biological specimens. Ultramicroscopy 109, 7080.

A.V. Crewe , J. Wall & J. Langmore (1970). Visibility of single atoms. Science 168, 13381340.

N. de Jonge , D.B. Peckys , G.J. Kremers & D.W. Piston (2009). Electron microscopy of whole cells in liquid with nanometer resolution. Proc Natl Acad Sci 106, 21592164.

N. de Jonge , N. Poirier-Demers , H. Demers , D.B. Peckys & D. Drouin (2010a). Nanometer-resolution electron microscopy through micrometers-thick water layers. Ultramicroscopy 110(9), 11141119.

N. de Jonge , R. Sougrat , B. Northan & S.J. Pennycook (2010b). Three-dimensional scanning transmission electron microscopy for biological specimen. Microsc Microanal 16(1), 5463.

D. Drouin , A.R. Couture , D. Joly , X. Tastet , V. Aimez & R. Gauvin (2007). CASINO V2.42—A fast and easy-to-use modeling tool for scanning electron microscopy and microanalysis users. Scanning 29(3), 92101.

L. Frank (2005). Noise in secondary electron emission: The low yield case. J Electron Microsc (Tokyo) 54(4), 361365.

M.F. Hohmann-Marriott , A.A. Sousa , A. Azari , S. Glushakova , G. Zhang , J. Zimmerberg & R.D. Leapman (2009). Nanoscale 3D cellular imaging by axial scanning transmission electron tomography. Nat Methods 6, 729732.

P. Hovington , D. Drouin & R. Gauvin (1997). CASINO: A new Monte Carlo code in C language for electron beam interaction—part I: Description of the program. Scanning 19(1), 114.

J.K. Hyun , P. Ercius & D.A. Muller (2008). Beam spreading and spatial resolution in thick organic specimens. Ultramicroscopy 109(1), 17.

D.C. Joy (1995). Monte Carlo Modeling for Electron Microscopy and Microanalysis. New York: Oxford University Press.

D.C. Joy & S. Luo (1989). An empirical stopping power relationship for low-energy electrons. Scanning 11, 176180.

E.J. Kirkland & M.G. Thomas (1996). A high efficiency annular dark field detector for STEM. Ultramicroscopy 62, 7988.

D.F. Kyser (1979). Monte Carlo simulation in analytical electron microscopy. In Introduction to Analytical Electron Microscopy, J.J. Hren , J.I. Goldstein & D.C. Joy (Eds.), pp. 199222. New York: Plenum Press.

S.A. Mueller & A. Engel (2006). Biological scanning transmission electron microscopy: Imaging and single molecule mass determination. Chimia 60, 749753.

P.D. Nellist , M.F. Chisholm , N. Dellby , O.L. Krivanek , M.F. Murfitt , Z.S. Szilagyi , A.R. Lupini , A. Borisevich , W.H. Sides & S.J. Pennycook (2004). Direct sub-angstrom imaging of a crystal lattice. Science 305, 1741.

R. Reichelt & A. Engel (1984). Monte Carlo calculations of elastic and inelastic electron scattering in biological and plastic materials. Ultramicroscopy 13(3), 279293.

L. Reimer (1998). Scanning Electron Microscopy: Physics of Image Formation and Microanalysis. New York: Springer.

F. Salvat , A. Jablonski & C.J. Powell (2005). ELSEPA—Dirac partial-wave calculation of elastic scattering of electrons and positrons by atoms, positive ions and molecules. Comput Phys Comm 165, 157190.

A.A. Sousa , M. Hohmann-Marriott , M.A. Aronova , G. Zhang & R.D. Leapman (2008). Determination of quantitative distributions of heavy-metal stain in biological specimens by annular dark-field STEM. J Struct Biol 162, 1428.

A.A. Sousa , M.F. Hohmann-Marriott , G. Zhang & R.D. Leapman (2009). Monte Carlo electron-trajectory simulations in bright-field and dark-field STEM: Implications for tomography of thick biological sections. Ultramicroscopy 109(3), 213221.

K. van Benthem , A.R. Lupini , M. Kim , H.S. Baik , S.J. Doh , J.H. Lee , M.P. Oxley , S.D. Findlay , L.J. Allen & S.J. Pennycook (2005). Three-dimensional imaging of individual hafnium atoms inside a semiconductor device. Appl Phys Lett 87, 034104-1034104-3.

D.B. Williams & C.B. Carter (1996). Transmission Electron Microscopy: A Textbook for Materials Science. New York: Plenum Press.

Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Microscopy and Microanalysis
  • ISSN: 1431-9276
  • EISSN: 1435-8115
  • URL: /core/journals/microscopy-and-microanalysis
Please enter your name
Please enter a valid email address
Who would you like to send this to? *