Ettention: building blocks for iterative reconstruction algorithms

Tim Dahmen, Lukas Marsalek, Nico Marniok, Beata Turonov√°, Sviatoslav Bogachev, Patrick Trampert, Stefan Nickels and Philipp Slusallek

We present a novel software package for tomographic reconstruction in electron microscopy, named Ettention. The software consists of a set of modular building-blocks for iterative reconstruction algorithms. 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 user interface. We provide developers with a clean 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. Several case studies are provided to demonstrate the feasibility of the concept.

Accepted to Proceddings of Microscopy & Microanalysis 2015, Portland, Oregan, 2. - 6. August 2015.

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