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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
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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 

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Footnotes

†

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

References

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