Three-dimensional chemical mapping by EFTEM-TomoJ including improvement of SNR by PCA and ART reconstruction of volume by noise suppression

Microscopy and Microanalysis

Volumn 19, Issue 6, 2013, Pages 1669-1677

  Messaoudi, Cédric ^a,b   Aschman, Nicolas ^a,b   Cunha, Marcel ^a,b,e   Oikawa, Tetsuo ^c   Sanchez Sorzano, Carlos O ^d   Marco, Sergio ^a,b  

^a INSTITUT CURIE   (France)

^b Centre Universitaire   (France)

^c JEOL LTD   (Japan)

^d UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

^e STATE UNIVERSITY OF RIO DE JANEIRO   (Brazil)

Author keywords

3D reconstruction; chemical mapping; EFTEM; electron tomography

Indexed keywords

ARTICLE; COMPUTER PROGRAM; ELECTRON TOMOGRAPHY; EQUIPMENT; METHODOLOGY; THREE DIMENSIONAL IMAGING;

ELECTRON MICROSCOPE TOMOGRAPHY; IMAGING, THREE-DIMENSIONAL; SOFTWARE;

EID: 84887890726     PISSN: 14319276     EISSN: 14358115     Source Type: Journal    
DOI: 10.1017/S1431927613013317     Document Type: Article

References (21)

1. 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.
2. 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.
3. BATENBURG, K.J. & SIJBERS, J. (2011). DART: A practical reconstruction algorithm for discrete tomography. IEEE Trans Image Process 20, 2542-2553.
4. BONNET, N. & LIEHN, J.C. (1988). Image registration in electron microscopy: Application of a robust method. J Electron Microsc Te c h 10, 27-33.
5. 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.
6. CUNHA, M.M., FRANZEN, A.J., ALVIANO, D.S., ZANARDI, E., ALVI-ANO, 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.
7. 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.
8. GORIS, B., ROELANDTS, T., BATENBURG, K.J., HEIDARI MEZERJI, H. & BALS, S. (2013). Advanced reconstruction algorithms for electron tomography: From comparison to combination. Ultra-microscopy 127, 40-47.
9. LEAPMAN, R.D., KOCSIS, E., ZHANG, G., TALBOT, T.L. & LAQUER-RIERE, P. (2004). Three-dimensional distributions of elements in biological samples by energy-filtered electron tomography. Ultramicroscopy 100, 115-125.
10. LOZANO-PEREZ, S., DE CASTRO BERNAL, V. & NICHOLLS, R.J. (2009). Achieving sub-nanometre particle mapping with energy-filtered TEM. Ultramicroscopy 109, 1217-1228.
11. 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.
12. 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.
13. 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.
14. 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.
15. QUINTANA, C., LECHAIRE, J.P., BONNET, N., RISCO, C. & CARRAS-COSA, J.L. (2001). Elemental maps from EFTEM images using two different background subtraction models. Microsc Res Tech 53, 147-156.
16. 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.
17. ROELANDTS, T., BATENBURG, K.J., BIERMANS, E., KÜBEL, C., BALS, S. & SIJBERS, J. (2012). Accurate segmentation of dense nano-particles by partially discrete electron tomography. Ultramicros-copy 114, 96-105.
18. SCHNEIDER, C.A., RASBAND, W.S. & ELICEIRI, K.W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9, 671-675.
19. 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.
20. VOLKMANN, N. (2010). Methods for segmentation and interpretation of electron tomographic reconstructions. Methods Enzy-mol 483, 31-46.
21. 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. Ultramicros-copy 122, 2-18.