Hostname: page-component-78c5997874-g7gxr Total loading time: 0 Render date: 2024-11-10T17:45:54.891Z Has data issue: false hasContentIssue false
  • English
  • Français

Three-Dimensional Chemical Mapping by EFTEM-TomoJ Including Improvement of SNR by PCA and ART Reconstruction of Volume by Noise Suppression

Published online by Cambridge University Press:  28 August 2013

Cédric Messaoudi ,
Nicolas Aschman ,
Marcel Cunha ,
Tetsuo Oikawa ,
Carlos O. Sanchez Sorzano  and
Sergio Marco
Cédric Messaoudi
Affiliation:
Institut Curie, Centre de Recherche, Bat 112, Centre Universitaire, 91405 Orsay Cedex, France INSERM U759, Bat 112, Centre Universitaire, 91405 Orsay Cedex, France
Nicolas Aschman
Affiliation:
Institut Curie, Centre de Recherche, Bat 112, Centre Universitaire, 91405 Orsay Cedex, France INSERM U759, Bat 112, Centre Universitaire, 91405 Orsay Cedex, France
Marcel Cunha
Affiliation:
Institut Curie, Centre de Recherche, Bat 112, Centre Universitaire, 91405 Orsay Cedex, France INSERM U759, Bat 112, Centre Universitaire, 91405 Orsay Cedex, France
Tetsuo Oikawa
Affiliation:
JEOL Ltd., 1-2 Musashino 3-chome, Akishima, Tokyo 196-8558, Japan
Carlos O. Sanchez Sorzano
Affiliation:
National Center of Biotechnology (CSIC), c/Darwin, 3. Campus Univ. Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain
Sergio Marco*
Affiliation:
Institut Curie, Centre de Recherche, Bat 112, Centre Universitaire, 91405 Orsay Cedex, France INSERM U759, Bat 112, Centre Universitaire, 91405 Orsay Cedex, France
*
*Corresponding author. E-mail: sergio.marco@curie.fr
Get access

Abstract

Electron tomography is becoming one of the most used methods for structural analysis at nanometric scale in biological and materials sciences. Combined with chemical mapping, it provides qualitative and semiquantitative information on the distribution of chemical elements on a given sample. Due to the current difficulties in obtaining three-dimensional (3D) maps by energy-filtered transmission electron microscopy (EFTEM), the use of 3D chemical mapping has not been widely adopted by the electron microscopy community. The lack of specialized software further complicates the issue, especially in the case of data with a low signal-to-noise ratio (SNR). Moreover, data interpretation is rendered difficult by the absence of efficient segmentation tools. Thus, specialized software for the computation of 3D maps by EFTEM needs to include optimized methods for image series alignment, algorithms to improve SNR, different background subtraction models, and methods to facilitate map segmentation. Here we present a software package (EFTEM-TomoJ, which can be downloaded from http://u759.curie.fr/fr/download/softwares/EFTEM-TomoJ), specifically dedicated to computation of EFTEM 3D chemical maps including noise filtering by image reconstitution based on multivariate statistical analysis. We also present an algorithm named BgART (for background removing algebraic reconstruction technique) allowing the discrimination between background and signal and improving the reconstructed volume in an iterative way.

Keywords

EFTEMelectron tomography3D reconstructionchemical mapping
Type
Techniques and Instrumentation Development
Information
Microscopy and Microanalysis , Volume 19 , Issue 6 , December 2013 , pp. 1669 - 1677
Copyright
Copyright © Microscopy Society of America 2013 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

†

Current address: Departamento de Biologia Celular, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Brazil

References

REFERENCES

Aronova, M.A., Kim, Y.C., Harmon, R., Sousa, A.A., Zhang, G. & Leapman, R.D. (2007). Three-dimensional elemental mapping of phosphorus by quantitative electron spectroscopic tomography (QuEST). J Struct Biol 160, 35–48.CrossRefGoogle ScholarPubMed
Aronova, M.A., Sousa, A.A., Zhang, G. & Leapman, R.D. (2010). Limitations of beam damage in electron spectroscopic tomography of embedded cells. J Microsc 239, 223–232.Google Scholar
Batenburg, K.J. & Sijbers, J. (2011). DART: A practical reconstruction algorithm for discrete tomography. IEEE Trans Image Process 20, 2542–2553.CrossRefGoogle Scholar
Bonnet, N. & Liehn, J.C. (1988). Image registration in electron microscopy: Application of a robust method. J Electron Microsc Tech 10, 27–33.Google Scholar
Boudier, T., Lechaire, J.P., Frébourg, G., Messaoudi, C., Mory, C., Colliex, C., Gaill, F. & Marco, S. (2005). A public software for energy filtering transmission electron tomography (EFTET-J): Application to the study of granular inclusions in bacteria from Riftia pachyptila. J Struct Biol 151, 151–159.CrossRefGoogle Scholar
Cunha, M.M., Franzen, A.J., Alviano, D.S., Zanardi, E., Alviano, C.S., De Souza, W. & Rozental, S. (2005). Inhibition of melanin synthesis pathway by tricyclazole increases susceptibility of Fonsecaea pedrosoi against mouse macrophages. Microsc Res Tech 68, 377–384.Google Scholar
Florea, I., Ersen, O., Arenal, R., Ihiawakrim, D., Messaoudi, C., Chizari, K., Janowska, I. & Pham-Huu, C. (2012). 3D analysis of the morphology and spatial distribution of nitrogen in nitrogen-doped carbon nanotubes by energy-filtered transmission electron microscopy tomography. J Am Chem Soc 134, 9672–9680.CrossRefGoogle ScholarPubMed
Goris, B., Roelandts, T., Batenburg, K.J., Heidari Mezerji, H. & Bals, S. (2013). Advanced reconstruction algorithms for electron tomography: From comparison to combination. Ultramicroscopy 127, 40–47.Google Scholar
Leapman, R.D., Kocsis, E., Zhang, G., Talbot, T.L. & Laquerriere, P. (2004). Three-dimensional distributions of elements in biological samples by energy-filtered electron tomography. Ultramicroscopy 100, 115–125.Google Scholar
Lozano-Perez, S., de Castro Bernal, V. & Nicholls, R.J. (2009). Achieving sub-nanometre particle mapping with energy-filtered TEM. Ultramicroscopy 109, 1217–1228.CrossRefGoogle ScholarPubMed
Messaoudi, C., Boudier, T., Sorzano, C.O. & Marco, S. (2007). TomoJ: Tomography software for three-dimensional reconstruction in transmission electron microscopy. BMC Bioinformatics 8, 288–297.CrossRefGoogle Scholar
Midgley, P.A. & Weyland, M. (2003). 3D electron microscopy in the physical sciences: The development of Z-contrast and EFTEM tomography. Ultramicroscopy 96, 413–431.Google Scholar
Möbus, G. & Inkson, B.J. (2001). Three-dimensional reconstruction of buried nanoparticles by element-sensitive tomography based on inelastically scattered electrons. Appl Phys Lett 79, 1369–1371.CrossRefGoogle Scholar
Pluim, J.P., Maintz, J.B. & Viergever, M.A. (2003). Mutual-information-based registration of medical images: A survey. IEEE Trans Med Imaging 22, 986–1004.Google Scholar
Quintana, C., Lechaire, J.P., Bonnet, N., Risco, C. & Carrascosa, J.L. (2001). Elemental maps from EFTEM images using two different background subtraction models. Microsc Res Tech 53, 147–156.CrossRefGoogle ScholarPubMed
Quintana, C., Marco, S., Bonnet, N., Risco, C., Gutiérrez, M.L., Guerrero, A. & Carrascosa, J.L. (1998). Optimization of phosphorus localization by EFTEM of nucleic acid containing structures. Micron 29, 297–307.CrossRefGoogle ScholarPubMed
Roelandts, T., Batenburg, K.J., Biermans, E., Kübel, C., Bals, S. & Sijbers, J. (2012). Accurate segmentation of dense nanoparticles by partially discrete electron tomography. Ultramicroscopy 114, 96–105.CrossRefGoogle ScholarPubMed
Schneider, C.A., Rasband, W.S. & Eliceiri, K.W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9, 671–675.Google Scholar
Sorzano, C.O., 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, 124–135.CrossRefGoogle ScholarPubMed
Volkmann, N. (2010). Methods for segmentation and interpretation of electron tomographic reconstructions. Methods Enzymol 483, 31–46.Google Scholar
Yedra, L., Eljarrat, A., Arenal, R., Pellicer, E., Cabo, M., López-Ortega, A., Estrader, M., Sort, J., Baró, M.D., Estradé, S. & Peiró, F. (2012). EEL spectroscopic tomography: Towards a new dimension in nanomaterials analysis. Ultramicroscopy 122, 2–18.CrossRefGoogle ScholarPubMed

Messaoudi et al. supplementary video

Movie 1

Download Messaoudi et al. supplementary video(Video)
Video 32.5 MB

Messaoudi et al. supplementary video

Movie 2

Download Messaoudi et al. supplementary video(Video)
Video 43.5 MB

Messaoudi et al. supplementary video

Movie 3

Download Messaoudi et al. supplementary video(Video)
Video 8.2 MB
Supplementary material: PDF

Messaoudi et al. supplementary material

Supplementary material

Download Messaoudi et al. supplementary material(PDF)
PDF 826 KB