Hundreds of thousands of images turned into 3D reconstructions in ULTRA fast time

17 November 2016

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Erica Yang, Head of Visualisation at STFC’s Scientific Computing Department by the video of ULTRA which is being displayed on the main screens at SC16, the World’s largest supercomputing conference being attended by STFC.

(Credit: STFC)


UK researchers have developed a new way of processing hundreds of thousands of images of a rotating object such that they can then turn them into a complete 3D visual reconstruction of the subject with unprecedented detail.

With scientific experiments producing increasing amounts of data, the demand for significant processing power is higher than ever and can only be achieved through data intensive techniques.

A new system called ULTRA which has been developed by computing experts at the Science and Technology Facilities Council means that within tens of minutes, scientists can have hundreds of digital replicas of a sample of interest, inside and out, depicting layers and segments of the internal details at a resolution not achievable before.

A typical 3D reconstruction which is vital for gaining a more thorough understanding of an object of interest can already be done in minutes using one of the most common and fast existing algorithms, the Filtered Back Projection (FBP) algorithm. However, where there is a need to scan an object from different angles across different energy ranges to reveal contrasts within the article, iterative algorithms are needed.

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Segmented 3D Volume Images with Isolated Beads in Different Colours/Materials.
(Credit:
SophiaBeads Dataset Project/The ULTRA team)
Iterative algorithms typically run slower than the FBP algorithm, taking 100s of minutes to run. However, the new ULTRA platform speeds up that process:

“Our system not only speeds up the process of reconstruction, saving hours of experimental time, it also provides a wider range of computational intensive algorithms to reconstruct scans; for example in cases where there are missing angles”, said Erica Yang, Head of Visualisation at STFC’s Scientific Computing Department.

The insight obtained using ULTRA can then be used to steer the next experiment step, for example, to adjust sample positions and beam alignment, or to decide whether to use different reconstruction algorithms or parameters, or image filters.

ULTRA is currently being tested with STFC’s ISIS Neutron and Muon Source - a research facility housing a suite of giant microscopes, or instruments - that enable scientists to see things at the atomic level. However, it has the potential to be exploited in other experimental facilities.

Notes to editors

Contacts

  • Lucy Stone, STFC Communications team
  • Erica Yang, Head of Visualisation at STFC’s Scientific Computing Department

STFC’s Scientific Computing Department

The Scientific Computing Department develops and utilises its expertise and relationships to establish leadership positions on the provision and support of scientific computing infrastructures and the research and development of scientific applications. This increases the UK’s scientific and economic impact by the creation of innovative solutions.

Thousands of 3D image stacks, one per energy band.
(Credit: The STFC’s SCD ULTRA team)

The department provides large scale HPC facilities, computing data services and infrastructure at both STFC Daresbury Laboratory and STFC’s Rutherford Appleton Laboratory.

The department also includes world leading experts in a number of scientific fields including computational chemistry, computational engineering, materials science, band theory, computational biology, advanced research computing, atomic and molecular physics, numerical analysis, software engineering, data services, petascale storage, scientific information and scientific computing technology.

STFC’s ISIS Neutron and Muon source

Visit the ISIS Neutron and Muon source (link opens in a new window) website.

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