Tag Archives: Team Computational 3D Imaging


NOTOX is one of the building block projects of the European research initiative SEURAT (safety evaluation ultimately replacing animal testing) funded by EU-FP7 HEALTH programme and the European Cosmetics Association (Cosmetics Europe). The total funding for the cluster projects is 50 million €. This initiative with six projects as building blocks aims at the common strategy “towards the replacement of current repeated dose systemic toxicity testing in human safety assessment”.

Tomographic reconstruction of an electron tomography tilt series. Image from [1].

DFKI Participated in NOTOX by providing high performance implementations of iterative tomographic reconstruction algorithms for electron tomography using the Ettention software package.

[1] T. Dahmen et al., The Ettention software package, Ultramicroscopy 161 (2016) 110–118.

IMCL – Iterative Methods for Computed Laminography

Standard 3D Computed Tomography (3D-CT) is an established technique both in medicine and non-destructive industrial testing. However, some very important and safety-critical objects, like airplane wings, printed circuit boards or fiber-reinforced lighweight construction structures cannot be appropriately examined using 3D-CT.

Geometry of the CLARA Laminography device. Image from [1].

We are building a novel pipeline based on Computed Laminography(CL) to allow for a robust and reliable non-destructive testing of these objects, drawing on the excellence of our team in industrial engineering, mathematical algorithm development and highly-efficient parallel software implementations.

Laminographic reconstruction using different reconstruction settings. Image from [1].

[1] P. Trampert et al., Spherically symmetric volume elements as basis functions for image reconstructions in computed laminography, J. Xray. Sci. Technol. Preprint (2017) 1–14.



Individualisierte Implantate und Prothesen für die Versorgung unterer Extremitäten (IIP-EXTREM)

Individualisierte Implantate und Prothesen für die Versorgung unterer Extremitäten (IIP-EXTREM)

Severe injuries of the lower leg require individual treatment and often require the treating doctors to make difficult decisions. The funded research project  IIP-EXTREM in the BMB+F program „Individualized Medical Technology“ aims to provide technical support for those decisions and make them more quantitative.

The project follows two strategies: the first strategy aims for reconstruction using individualized and standardized implants. Powerful simulations and visualizations based on clinical CT or MRT data will help to re-orient bone fragments, make decisions concerning the right choice of implant and finally generate individual implants. The fabrication of the implants will be performed using modern methods of additive metal fabrication.

The second strategy will come in place if a severe injury makes an amputation inevitable. In this case, simulation software  will help to create an exact fitting, high performance prothesis shaft.

Both subprojects aim to use efficient simulations and modern additive manufacturing methods to optimize the production chain and save expensive recurring treatments.

The clinical side of the consortium is represented by the Chair of Orthopedics of the Trauma Surgery of the university Witten/Herdecke. The simulation and its validation is developed jointly between the Chair of Applied Mechanics of Saarland University and the German Research Center for Artificial Intelligence (DFKI), that also creates the user interfaces. Individualized implants are developed and manufactured by Karl Leibinger Medizintechnik GmbH & Co. KG, the prothesis shafts are developed and manufactured by Ottobock HealthCare GmbH, who also coordinates the consortium.

Project duration: 01.06.2016 – ???

Contact: Dr Tim Dahmen



Ettention is a software package for tomographic reconstruction in electron tomography. It implements the algorithms simultaneous algebraic reconstruction technique (SART), simultaneous iterative reconstruction technique (SIRT) and a generic, block-iterative reconstruction algorithm. Ettention is written in C++ and internally uses OpenCL to run on a large number of high-performance computing.

Tomographic reconstructions performed using the Ettention software package. Images from [1].

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Computational 3D Imaging

Team Computational 3D Imaging

The team conducts bleeding edge research on algorithmic questions with different applications in microscopy and three-dimensional imaging. The broader research question is: how can one obtain a maximum of information about a sample? Hereby, we consider several aspects of 3D imaging. How can we incorporate different kind of prior knowledge about the microscope, the specimen, or the physics of image formation into reconstruction algorithms to obtain better reconstructions from existing projections? What are optimal recording schemes to obtain 3D information? Specifically, how can adaptive sampling schemes augment the information content of a dataset already during the acquisition? And finally: how can simulations be used to make  physical quantities that can not easily be observed directly, appear in a three-dimensional dataset. For example, can we use finite element simulations to enhance a tomogram with residual stress vectors?

Scanning Electron Microscope image of cast iron acquired using an adaptive scanning method.

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