The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography

doi:10.1016/j.ultramic.2015.05.002

. 2015 Oct:157:35-47.

doi: 10.1016/j.ultramic.2015.05.002. Epub 2015 May 6.

The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography

Wim van Aarle¹, Willem Jan Palenstijn², Jan De Beenhouwer³, Thomas Altantzis⁴, Sara Bals⁵, K Joost Batenburg⁶, Jan Sijbers⁷

Affiliations

¹ iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium. Electronic address: wim.vanaarle@uantwerpen.be.
² iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Centrum Wiskunde & Informatica, Science Park 123, NL-1098 XG Amsterdam, The Netherlands. Electronic address: willemjan.palenstijn@uantwerpen.be.
³ iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium. Electronic address: jan.debeenhouwer@uantwerpen.be.
⁴ Electron Microscopy for Materials Science, University of Antwerp, Groenenborgerlaan 171, B-2020 Wilrijk, Belgium. Electronic address: thomas.altantzis@uantwerpen.be.
⁵ Electron Microscopy for Materials Science, University of Antwerp, Groenenborgerlaan 171, B-2020 Wilrijk, Belgium. Electronic address: sara.bals@uantwerpen.be.
⁶ iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Centrum Wiskunde & Informatica, Science Park 123, NL-1098 XG Amsterdam, The Netherlands; Mathematical Institute, Leiden University, P.O. Box 9512, NL-2300 RA Leiden, The Netherlands. Electronic address: joost.batenburg@cwi.nl.
⁷ iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium. Electronic address: jan.sijbers@uantwerpen.be.

PMID: 26057688
DOI: 10.1016/j.ultramic.2015.05.002

The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography

Wim van Aarle et al. Ultramicroscopy. 2015 Oct.

. 2015 Oct:157:35-47.

doi: 10.1016/j.ultramic.2015.05.002. Epub 2015 May 6.

Authors

Wim van Aarle¹, Willem Jan Palenstijn², Jan De Beenhouwer³, Thomas Altantzis⁴, Sara Bals⁵, K Joost Batenburg⁶, Jan Sijbers⁷

Affiliations

¹ iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium. Electronic address: wim.vanaarle@uantwerpen.be.
² iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Centrum Wiskunde & Informatica, Science Park 123, NL-1098 XG Amsterdam, The Netherlands. Electronic address: willemjan.palenstijn@uantwerpen.be.
³ iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium. Electronic address: jan.debeenhouwer@uantwerpen.be.
⁴ Electron Microscopy for Materials Science, University of Antwerp, Groenenborgerlaan 171, B-2020 Wilrijk, Belgium. Electronic address: thomas.altantzis@uantwerpen.be.
⁵ Electron Microscopy for Materials Science, University of Antwerp, Groenenborgerlaan 171, B-2020 Wilrijk, Belgium. Electronic address: sara.bals@uantwerpen.be.
⁶ iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Centrum Wiskunde & Informatica, Science Park 123, NL-1098 XG Amsterdam, The Netherlands; Mathematical Institute, Leiden University, P.O. Box 9512, NL-2300 RA Leiden, The Netherlands. Electronic address: joost.batenburg@cwi.nl.
⁷ iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium. Electronic address: jan.sijbers@uantwerpen.be.

PMID: 26057688
DOI: 10.1016/j.ultramic.2015.05.002

Abstract

We present the ASTRA Toolbox as an open platform for 3D image reconstruction in tomography. Most of the software tools that are currently used in electron tomography offer limited flexibility with respect to the geometrical parameters of the acquisition model and the algorithms used for reconstruction. The ASTRA Toolbox provides an extensive set of fast and flexible building blocks that can be used to develop advanced reconstruction algorithms, effectively removing these limitations. We demonstrate this flexibility, the resulting reconstruction quality, and the computational efficiency of this toolbox by a series of experiments, based on experimental dual-axis tilt series.

Keywords: ASTRA Toolbox; Dual-axis; Electron tomography; Reconstruction.

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The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography

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The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography

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