Beyond filtered backprojection: a reconstruction software package for ion beam microtomography data

Habchi, C. and Gordillo Garcia, Nuria and Bourret, Stéphane and Barberet, Philippe and Jovet, C. and Moretto, Philippe and Seznec, H. (2013). Beyond filtered backprojection: a reconstruction software package for ion beam microtomography data. "Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms", v. 295 ; pp. 42-49. ISSN 0168-583X. https://doi.org/10.1016/j.nimb.2012.10.006.

Description

Title: Beyond filtered backprojection: a reconstruction software package for ion beam microtomography data
Author/s:
  • Habchi, C.
  • Gordillo Garcia, Nuria
  • Bourret, Stéphane
  • Barberet, Philippe
  • Jovet, C.
  • Moretto, Philippe
  • Seznec, H.
Item Type: Article
Título de Revista/Publicación: Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms
Date: January 2013
ISSN: 0168-583X
Volume: 295
Subjects:
Freetext Keywords: Ion beam tomography; 3D imaging; Filtered backprojection; MLEM; OSEM; ImageJ
Faculty: E.T.S.I. Industriales (UPM)
Department: Ingeniería Nuclear [hasta 2014]
Creative Commons Licenses: Recognition - No derivative works - Non commercial

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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.

More information

Item ID: 25704
DC Identifier: http://oa.upm.es/25704/
OAI Identifier: oai:oa.upm.es:25704
DOI: 10.1016/j.nimb.2012.10.006
Official URL: http://www.sciencedirect.com/science/article/pii/S0168583X12006350
Deposited by: Memoria Investigacion
Deposited on: 18 May 2014 12:12
Last Modified: 01 Feb 2015 23:56
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