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The Ettention software package

Tim Dahmen; Lukas Marsalek; Nico Marniok; Beata Turoňová; Sviatoslav Bogachev; Patrick Trampert; Stefan Nickels; Philipp Slusallek
In: Ultramicroscopy, Vol. n.a. Page n.a. Elsevier, 2015.


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 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 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. Several case studies are provided to demonstrate the feasibility of the concept.


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