title: The Ettention software package.
abstract: We present a novel software package for the problem "reconstruction from projections" in electron microscopy. The Ettention framework consists of a set of modular building-blocks for tomographic reconstruction algorithms. The well-known block iterative reconstruction method based on Kaczmarz algorithm is implemented using these building-blocks, including adaptations specific to electron tomography. Ettention simultaneously features (1) a modular, object-oriented software design, (2) optimized access to high-performance computing (HPC) platforms such as graphic processing units (GPU) or many-core architectures like Xeon Phi, and (3) accessibility to microscopy end-users via integration in the IMOD package and eTomo user interface. We also provide developers with a clean and well-structured application programming interface (API) that allows for extending the software easily and thus makes it an ideal platform for algorithmic research while hiding most of the technical details of high-performance computing.
authors.affiliation: German Research Center for Artificial Intelligence GmbH (DFKI), 66123 Saarbrücken, Germany; Saarland University, 66123 Saarbrücken, Germany. Electronic address: Tim.Dahmen@dfki.de.
authors.forename: Tim
authors.initials: T
authors.lastname: Dahmen
authors.affiliation: Eyen SE, Na Nivách 1043/16, 141 00 Praha 4, Czech Republic; Saarland University, 66123 Saarbrücken, Germany.
authors.forename: Lukas
authors.initials: L
authors.lastname: Marsalek
authors.affiliation: Saarland University, 66123 Saarbrücken, Germany.
authors.forename: Nico
authors.initials: N
authors.lastname: Marniok
authors.affiliation: Saarland University, 66123 Saarbrücken, Germany; IMPRS-CS, Max-Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken, Germany.
authors.forename: Beata
authors.initials: B
authors.lastname: Turoňová
authors.affiliation: Saarland University, 66123 Saarbrücken, Germany.
authors.forename: Sviatoslav
authors.initials: S
authors.lastname: Bogachev
authors.affiliation: German Research Center for Artificial Intelligence GmbH (DFKI), 66123 Saarbrücken, Germany.
authors.forename: Patrick
authors.initials: P
authors.lastname: Trampert
authors.affiliation: German Research Center for Artificial Intelligence GmbH (DFKI), 66123 Saarbrücken, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Nickels
authors.affiliation: German Research Center for Artificial Intelligence GmbH (DFKI), 66123 Saarbrücken, Germany; Saarland University, 66123 Saarbrücken, Germany.
authors.forename: Philipp
authors.initials: P
authors.lastname: Slusallek
keywords: Block iterative methods; Electron tomography; GPU; High performance computing; OpenCL; Software architecture; Tomographic reconstruction