DOI: 10.1017/s1431927613013317. Three-Dimensional Chemical Mapping by EFTEM-TomoJ Including Improvement of SNR by PCA and ART Reconstruction of Volume by Noise Suppression

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

10.1017/s1431927613013317

Crossref journal-article

Oxford University Press (OUP)

Microscopy and Microanalysis (286)

Abstract

AbstractElectron 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.

Bibliography

Messaoudi, C., Aschman, N., Cunha, M., Oikawa, T., Sorzano, C. O. S., & Marco, S. (2013). Three-Dimensional Chemical Mapping by EFTEM-TomoJ Including Improvement of SNR by PCA and ART Reconstruction of Volume by Noise Suppression. Microscopy and Microanalysis, 19(6), 1669â1677.

Authors 6

Cédric Messaoudi (first)
Nicolas Aschman (additional)
Marcel Cunha (additional)
Tetsuo Oikawa (additional)
Carlos O. Sanchez Sorzano (additional)
Sergio Marco (additional)

References 21 Referenced 27

Dates

Type	When
Created	11 years, 11 months ago (Aug. 28, 2013, 4 a.m.)
Deposited	2 years, 6 months ago (Feb. 14, 2023, 3:36 p.m.)
Indexed	1 year ago (Aug. 5, 2024, 2:38 a.m.)
Issued	11 years, 11 months ago (Aug. 28, 2013)
Published	11 years, 11 months ago (Aug. 28, 2013)
Published Online	11 years, 11 months ago (Aug. 28, 2013)
Published Print	11 years, 8 months ago (Dec. 1, 2013)

Funders 0

None

BibTeX

@article{Messaoudi_2013, title={Three-Dimensional Chemical Mapping by EFTEM-TomoJ Including Improvement of SNR by PCA and ART Reconstruction of Volume by Noise Suppression}, volume={19}, ISSN={1435-8115}, url={http://dx.doi.org/10.1017/s1431927613013317}, DOI={10.1017/s1431927613013317}, number={6}, journal={Microscopy and Microanalysis}, publisher={Oxford University Press (OUP)}, author={Messaoudi, Cédric and Aschman, Nicolas and Cunha, Marcel and Oikawa, Tetsuo and Sorzano, Carlos O. Sanchez and Marco, Sergio}, year={2013}, month=aug, pages={1669–1677} }

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