title: Self-adapting denoising, alignment and reconstruction in electron tomography in materials science.
abstract: An automatic procedure for electron tomography is presented. This procedure is adapted for specimens that can be fashioned into a needle-shaped sample and has been evaluated on inorganic samples. It consists of self-adapting denoising, automatic and accurate alignment including detection and correction of tilt axis, and 3D reconstruction. We propose the exploitation of a large amount of information of an electron tomography acquisition to achieve robust and automatic mixed Poisson-Gaussian noise parameter estimation and denoising using undecimated wavelet transforms. The alignment is made by mixing three techniques, namely (i) cross-correlations between neighboring projections, (ii) common line algorithm to get a precise shift correction in the direction of the tilt axis and (iii) intermediate reconstructions to precisely determine the tilt axis and shift correction in the direction perpendicular to that axis. Mixing alignment techniques turns out to be very efficient and fast. Significant improvements are highlighted in both simulations and real data reconstructions of porous silicon in high angle annular dark field mode and agglomerated silver nanoparticles in incoherent bright field mode. 3D reconstructions obtained with minimal user-intervention present fewer artefacts and less noise, which permits easier and more reliable segmentation and quantitative analysis. After careful sample preparation and data acquisition, the denoising procedure, alignment and reconstruction can be achieved within an hour for a 3D volume of about a hundred million voxels, which is a step toward a more routine use of electron tomography.
authors.affiliation: Université Grenoble Alpes, F-38000 Grenoble, France; CEA, LETI, MINATEC Campus, F-38054 Grenoble, France. Electronic address: tony.printemps@cea.fr.
authors.forename: Tony
authors.initials: T
authors.lastname: Printemps
authors.affiliation: Dipartimento di Fisica, Università di Cagliari, Cittadella Universitaria, S.P. 8km 0.700, 09042 Monserrato (Ca), Italy.
authors.forename: Guido
authors.initials: G
authors.lastname: Mula
authors.affiliation: Université Grenoble Alpes, F-38000 Grenoble, France; CEA, LETI, MINATEC Campus, F-38054 Grenoble, France.
authors.forename: Daniele
authors.initials: D
authors.lastname: Sette
authors.affiliation: Université Grenoble Alpes, F-38000 Grenoble, France; CEA, LETI, MINATEC Campus, F-38054 Grenoble, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Bleuet
authors.affiliation: Université Grenoble Alpes, F-38000 Grenoble, France; CEA, LETI, MINATEC Campus, F-38054 Grenoble, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Delaye
authors.affiliation: Université Grenoble Alpes, F-38000 Grenoble, France; CEA, LETI, MINATEC Campus, F-38054 Grenoble, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Bernier
authors.affiliation: Université Grenoble Alpes, F-38000 Grenoble, France; CEA, LETI, MINATEC Campus, F-38054 Grenoble, France.
authors.forename: Adeline
authors.initials: A
authors.lastname: Grenier
authors.affiliation: Université Grenoble Alpes, F-38000 Grenoble, France; CEA, LETI, MINATEC Campus, F-38054 Grenoble, France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Audoit
authors.affiliation: Université Grenoble Alpes, F-38000 Grenoble, France; CEA, LETI, MINATEC Campus, F-38054 Grenoble, France.
authors.forename: Narciso
authors.initials: N
authors.lastname: Gambacorti
authors.affiliation: Université Grenoble Alpes, F-38000 Grenoble, France; CEA, LETI, MINATEC Campus, F-38054 Grenoble, France.
authors.forename: Lionel
authors.initials: L
authors.lastname: Hervé
keywords: Denoising; Electron tomography; IBF; Porous silicon; Silver nanoparticles; Wavelet