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Combined Scanning Transmission Electron Microscopy Tilt- and Focal Series

Published online by Cambridge University Press:  19 February 2014

Tim Dahmen ,
Jean-Pierre Baudoin ,
Andrew R. Lupini ,
Christian Kübel ,
Philipp Slusallek  and
Niels de Jonge
Tim Dahmen
Affiliation:
German Research Center for Artificial Intelligence GmbH (DFKI), 66123 Saarbrücken, Germany
Jean-Pierre Baudoin
Affiliation:
Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232-0615, USA
Andrew R. Lupini
Affiliation:
Karlsruhe Institute for Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
Christian Kübel
Affiliation:
Karlsruhe Institute for Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
Philipp Slusallek
Affiliation:
German Research Center for Artificial Intelligence GmbH (DFKI), 66123 Saarbrücken, Germany
Niels de Jonge*
Affiliation:
Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232-0615, USA Leibniz Institute for New Materials (INM), 66123 Saarbrücken, Germany
*
*Corresponding author. niels.dejonge@inm-gmbh.de
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Abstract

In this study, a combined tilt- and focal series is proposed as a new recording scheme for high-angle annular dark-field scanning transmission electron microscopy (STEM) tomography. Three-dimensional (3D) data were acquired by mechanically tilting the specimen, and recording a through-focal series at each tilt direction. The sample was a whole-mount macrophage cell with embedded gold nanoparticles. The tilt–focal algebraic reconstruction technique (TF-ART) is introduced as a new algorithm to reconstruct tomograms from such combined tilt- and focal series. The feasibility of TF-ART was demonstrated by 3D reconstruction of the experimental 3D data. The results were compared with a conventional STEM tilt series of a similar sample. The combined tilt- and focal series led to smaller “missing wedge” artifacts, and a higher axial resolution than obtained for the STEM tilt series, thus improving on one of the main issues of tilt series-based electron tomography.

Keywords

STEMtomography3Dfocal serieswhole cellnanoparticleSART3D reconstructionback projection
Type
Biological Applications
Information
Microscopy and Microanalysis , Volume 20 , Issue 2 , April 2014 , pp. 548 - 560
Copyright
© Microscopy Society of America 2014 

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Footnotes

†

Current address: La Timone Hospital and Medicine School, Marseille, France

References

Andersen, A.H. & Kak, A.C. (1984). Simultaneous algebraic reconstruction technique (SART): A superior implementation of the art algorithm. Ultrason Imaging 6, 81–94.Google Scholar
Aoyama, K., Takagi, T., Hirase, A. & Miyazawa, A. (2008). STEM tomography for thick biological specimens. Ultramicroscopy 109, 70–80.Google Scholar
Batenburg, K.J., Bals, S., Sijbers, J., Kübel, C., Midgley, P.A., Hernandez, J.C., Kaiser, U., Encina, E.R., Coronado, E.A. & Van Tendeloo, G. (2009). 3D imaging of nanomaterials by discrete tomography. Ultramicroscopy 109, 730–740.Google Scholar
Baudoin, J.-P., Jerome, W.G., Kübel, C. & de Jonge, N. (2013). Whole-cell analysis of low-density lipoprotein uptake by macrophages using STEM tomography. PloS One 8, e55022.Google Scholar
Baudoin, J.-P., Jinschek, J.R., Boothroyd, C.B., Dunin-Borkowski, R.E. & de Jonge, N. (2013). Chromatic aberration-corrected tilt series transmission electron microscopy of nanoparticles in a whole mount macrophage cell. Microsc Microanal 19, 814–820.Google Scholar
Behan, G., Cosgriff, E.C., Kirkland, A.I. & Nellist, P.D. (2009). Three-dimensional imaging by optical sectioning in the aberration-corrected scanning transmission electron microscope. Phil Trans R Soc A 367, 3825–3844.Google Scholar
Borisevich, A.Y., Lupini, A.R. & Pennycook, S.J. (2006). Depth sectioning with the aberration-corrected scanning transmission electron microscope. Proc Natl Acad Sci 103, 3044–3048.Google Scholar
Censor, Y. (1990). On variable block algebraic reconstruction techniques. In Mathematical Methods in Tomography, Dold, H.A. (Ed.), pp. 133–140. Oberwolfach, Germany: Springer-Verlag.Google Scholar
Cook, R.L. (1986). Stochastic sampling in computer graphics. ACM Trans Graph 5, 51–72.CrossRefGoogle Scholar
Denk, W. & Horstmann, H. (2004). Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biol 2, e329.Google Scholar
Dukes, M.J., Ramachandra, R., Baudoin, J.-P., Gray Jerome, W. & de Jonge, N. (2011). Three-dimensional locations of gold-labeled proteins in a whole mount eukaryotic cell obtained with 3nm precision using aberration-corrected scanning transmission electron microscopy. J Struct Biol 174, 552–562.Google Scholar
Engel, A. & Colliex, C. (1993). Application of scanning transmission electron microscopy to the study of biological structure. Curr Opin Biotechnol 4, 403–411.Google Scholar
Fernandez, J.J. (2012). Computational methods for electron tomography. Micron 43, 1010–1030.Google Scholar
Frank, J. (2006). Three-Dimensional Electron Microscopy of Macromolecular Assemblies : Visualization of Biological Molecules in Their Native State. Oxford, UK: Oxford University Press.Google Scholar
Frigo, S.P., Levine, Z.H. & Zaluzec, N.J. (2002). Submicron imaging of buried integrated circuit structures using scanning confocal electron microscopy. Appl Phys Lett 81, 2112.CrossRefGoogle Scholar
Gilbert, P. (1972). Iterative methods for the three-dimensional reconstruction of an object from projections. J Theor Biol 36, 105–117.Google Scholar
Gordon, R., Bender, R. & Herman, G.T. (1970). Algebraic reconstruction techniques (ART) for three-dimensional electron microscopy and x-ray photography. J Theor Biol 29, 471–481.Google Scholar
Goris, B., Van den Broek, W., Batenburg, K.J., Heidari Mezerji, H. & Bals, S. (2012). Electron tomography based on a total variation minimization reconstruction technique. Ultramicroscopy 113, 120–130.Google Scholar
Gregor, J. & Benson, T. (2008). Computational analysis and improvement of SIRT. IEEE Trans Med Imaging 27, 918–924.Google Scholar
Hell, S.W. (2007). Far-field optical nanoscopy. Science 316, 1153–1158.Google Scholar
Heymann, J.A.W., Hayles, M., Gestmann, I., Giannuzzi, L.A., Lich, B. & Subramaniam, S. (2006). Site-specific 3D imaging of cells and tissues with a dual beam microscope. J Struct Biol 155, 63–73.CrossRefGoogle ScholarPubMed
Hoenger, A. & McIntosh, J.R. (2009). Probing the macromolecular organization of cells by electron tomography. Curr Opin Cell Biol 21, 89–96.Google Scholar
Hohmann-Marriott, M.F., Sousa, A.A., Azari, A.A., Glushakova, S., Zhang, G., Zimmerberg, J. & Leapman, R.D. (2009). Nanoscale 3D cellular imaging by axial scanning transmission electron tomography. Nat Methods 6, 729–731.Google Scholar
Jerome, W.G., Cox, B.E., Griffin, E.E. & Ullery, J.C. (2008). Lysosomal cholesterol accumulation inhibits subsequent hydrolysis of lipoprotein cholesteryl ester. Microsc Microanal 14, 138–149.Google Scholar
De Jonge, N., Sougrat, R., Northan, B.M. & Pennycook, S.J. (2010). Three-dimensional scanning transmission electron microscopy of biological specimens. Microsc Microanal 16, 54–63.Google Scholar
Koster, A.J., Grimm, R., Typke, D., Hegerl, R., Stoschek, A., Walz, J. & Baumeister, W. (1997). Perspectives of molecular and cellular electron tomography. J Struct Biol 120, 276–308.Google Scholar
Kourkoutis, L.F., Plitzko, J.M. & Baumeister, W. (2012). Electron microscopy of biological materials at the nanometer scale. Ann Rev Mater Res 42, 33–58.Google Scholar
Kremer, J.R., Mastronarde, D.N. & McIntosh, J.R. (1996). Computer visualization of three-dimensional image data using IMOD. J Struct Biol 116, 71–76.Google Scholar
Kübel, C., Voigt, A., Schoenmakers, R., Otten, M., Su, D., Lee, T.-C., Carlsson, A. & Bradley, J. (2005). Recent advances in electron tomography: TEM and HAADF-STEM tomography for materials science and semiconductor applications. Microsc Microanal 11, 378–400.CrossRefGoogle ScholarPubMed
Lawrence, M.C. (1992). Least-Squares Method of Alignment Using Markers. In Electron Tomography, Frank, J. (Ed.), pp. 197–204. USA: Springer.Google Scholar
Levoy, M. (1990). Efficient ray tracing of volume data. ACM Trans Graph 9, 245–261.Google Scholar
Lupini, A.R. & de Jonge, N. (2011). The three-dimensional point spread function of aberration-corrected scanning transmission electron microscopy. Microsc Microanal 17, 817–826.Google Scholar
Marabini, R., Herman, G.T. & Carazo, J.M. (1998). 3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs). Ultramicroscopy 72, 53–65.Google Scholar
Messaoudii, C., Boudier, T., Sanchez Sorzano, C.O. & Marco, S. (2007). TomoJ: Tomography software for three-dimensional reconstruction in transmission electron microscopy. BMC Bioinformatics 8, 288.Google Scholar
Meyer-Ilse, W., Hamamoto, D., Nair, A., Lelièvre, S.A., Denbeaux, G., Johnson, L., Pearson, A.L., Yager, D., Legros, M.A. & Larabell, C.A. (2001). High resolution protein localization using soft X-ray microscopy. J Microsc 201, 395–403.Google Scholar
Penczek, P., Marko, M., Buttle, K. & Frank, J. (1995). Double-tilt electron tomography. Ultramicroscopy 60, 393–410.Google Scholar
Ramachandra, R., Demers, H. & de Jonge, N. (2013). The influence of the sample thickness on the lateral and axial resolution of aberration-corrected scanning transmission electron microscopy. Microsc Microanal 19, 93–101.Google Scholar
Ramachandra, R. & de Jonge, N. (2012). Optimized deconvolution for maximum axial resolution in three-dimensional aberration-corrected scanning transmission electron microscopy. Microsc Microanal 18, 218–228.Google Scholar
Reimer, L. (1998). Scanning Electron Microscopy : Physics of Image Formation and Microanalysis . Berlin, Germany: Springer.Google Scholar
Ring, E.A., Peckys, D.B., Dukes, M.J., Baudoin, J.P. & de Jonge, N. (2011). Silicon nitride windows for electron microscopy of whole cells. J Microsc 243, 273–283.Google Scholar
Robert, C.P. & Casella, G. (2005). Monte Carlo Statistical Methods (Springer Texts in Statistics). Secaucus, NJ, USA: Springer-Verlag New York Inc.Google Scholar
Sorzano, C.O.S., Messaoudi, C., Eibauer, M., Bilbao-Castro, J.R., Hegerl, R., Nickell, S., Marco, S. & Carazo, J.M. (2009). Marker-free image registration of electron tomography tilt-series. BMC Bioinformatics 10, 124.Google Scholar
Sousa, A.A., Aronova, M.A., Kim, Y.C., Dorward, L.M., Zhang, G. & Leapman, R.D. (2007). On the feasibility of visualizing ultrasmall gold labels in biological specimens by STEM tomography. J Struct Biol 159, 507–522.Google Scholar
Weyland, M. & Midgley, P.A. (2003). Extending energy-filtered transmission electron microscopy (EFTEM) into three dimensions using electron tomography. Microsc Microanal 9, 542–555.CrossRefGoogle ScholarPubMed
Whitted, T. (1980). An improved illumination model for shaded display. Comm ACM 23, 343–349.Google Scholar
Xu, W., Xu, F., Jones, M., Keszthelyi, B., Sedat, J., Agard, D. & Mueller, K. (2010). High-performance iterative electron tomography reconstruction with long-object compensation using graphics processing units (GPUs). J Struct Biol 171, 142–153.Google Scholar
Yakushevska, A.E., Lebbink, M.N., Geerts, W.J.C., Spek, L., van Donselaar, E.G., Jansen, K.A., Humbel, B.M., Post, J.A., Verkleij, A.J. & Koster, A.J. (2007). STEM tomography in cell biology. J Struct Biol 159, 381–391.Google Scholar
Zemlin, F. (1989). Dynamic focussing for recording images from tilted samples in small-spot scanning with a transmission electron microscope. J Electron Microsc Tech 11, 251–257.Google Scholar
Zeng, G.L. & Gullberg, G.T. (2000). Unmatched projector/backprojector pairs in an iterative reconstruction algorithm. IEEE Trans Med Imaging 19, 548–555.Google Scholar

Dahmen Supplementary Material

Combined tilt- and focal series high annular dark field scanning transmission electron microscopy (STEM) data. The sample was a whole mount macrophage cell containing gold nanoparticles of two different sizes distributed in clusters throughout its volume. The movie represents the aligned data recorded for a tilt range of -40° to +40° in 5° increments, with a focal series at each tilt angle using focus steps of 50 nm.

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Video 9.5 MB

Dahmen Supplementary Material

Perspective rendering of the reconstructed tomogram of the same cellular region as shown in Movie S1. The signal intensity was color-coded. The tilt-focal algebraic reconstruction technique (TF-ART) was used for the three dimensional reconstruction.

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Video 22.7 MB
Supplementary material: File

Dahmen Supplementary Material

Movie Captions

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