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Gordillo, N.Author

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November 27, 2019
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Beyond filtered backprojection: A reconstruction software package for ion beam microtomography data

Publicated to: NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIONS WITH MATERIALS AND ATOMS. 295 42-49 - 2013-01-07 295(), DOI: 10.1016/j.nimb.2012.10.006

Authors:

Habchi, C.; Gordillo, N.; Bourret, S.; Barberet, Ph.; Jovet, C.; Moretto, Ph.; Seznec, H.;
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Affiliations

CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France - Author
Univ Bordeaux, CENBG, UMR 5797, F-33170 Gradignan, France - Author

Abstract

A new version of the TomoRebuild data reduction software package is presented, for the reconstruction of scanning transmission ion microscopy tomography (STIMT) and particle induced X-ray emission tomography (PIXET) images. First, we present a state of the art of the reconstruction codes available for ion beam microtomography. The algorithm proposed here brings several advantages. It is a portable, multi-platform code, designed in C++ with well-separated classes for easier use and evolution. Data reduction is separated in different steps and the intermediate results may be checked if necessary. Although no additional graphic library or numerical tool is required to run the program as a command line, a user friendly interface was designed in Java, as an ImageJ plugin. All experimental and reconstruction parameters may be entered either through this plugin or directly in text format files. A simple standard format is proposed for the input of experimental data. Optional graphic applications using the ROOT interface may be used separately to display and fit energy spectra. Regarding the reconstruction process, the filtered backprojection (FBP) algorithm, already present in the previous version of the code, was optimized so that it is about 10 times as fast. In addition, Maximum Likelihood Expectation Maximization (MLEM) and its accelerated version Ordered Subsets Expectation Maximization (OSEM) algorithms were implemented. A detailed user guide in English is available. A reconstruction example of experimental data from a biological sample is given. It shows the capability of the code to reduce noise in the sinograms and to deal with incomplete data, which puts a new perspective on tomography using low number of projections or limited angle. (C) 2012 Elsevier B.V. All rights reserved.
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Keywords

3d imagingAlgorithmFiltered backprojectionImagejIon beam tomographyMicroscopy tomographyMlemOsem

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIONS WITH MATERIALS AND ATOMS due to its progression and the good impact it has achieved in recent years, according to the agency Scopus (SJR), it has become a reference in its field. In the year of publication of the work, 2013, it was in position , thus managing to position itself as a Q1 (Primer Cuartil), in the category Instrumentation.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2026-04-25:

  • WoS: 9
  • Scopus: 11
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Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2026-04-25:

  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 19 (PlumX).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.
  • Assignment of a Handle/URN as an identifier within the deposit in the Institutional Repository: https://oa.upm.es/25704/

As a result of the publication of the work in the institutional repository, statistical usage data has been obtained that reflects its impact. In terms of dissemination, we can state that, as of

  • Views: 372
  • Downloads: 551
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Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: France.

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Awards linked to the item

This work has been partly supported by the European Community as an Integrating Activity Support of Public and Industrial Research Using Ion Beam Technology (SPIRIT) under EC contract no. 227012. C elegans experiments have been carried out in the frame of the ANR Program: Contaminants, Ecosystemes, Sante 2010, in the TITANIUMS project.
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