Report from CCPi for the Period 12 May 2014 to 8 January 2015

Prof Philip Withers 6 January 2015


The CCP in Tomographic Imaging is progressing and since the last 6-month report, on 13 May 2014, it has built on current activities to deliver new versions of the core codes, as well as delivered benefits specified from the mid-term review findings. The CCPi prioritises the two areas of reconstruction and quantitative analysis. It aims to provide the UK tomography community with a toolbox of algorithms that increases the quality and level of information that can be extracted by computer tomography. Key components continue to be to increase usage, training and software deposits, as well as integration of new iterative methods within the toolkits.

There has been changes in the core staffing for the quantitative analysis as Srikanth Nagella and Ron Fowler have stepped in to cover this development and porting work creating the core 1.5 FTE. Also since Spring 2014 Martin Turner has had a role in the secretariat position and with Erica Yang has been developing extra functionality in collaborating with the new IMAT tomographic beamline on the ISIS neutron spallation source.

There is growing links with the recently funded CCP PET/MR that employs similar iterative solutions for positron emission tomography (PET) solutions. This has initially involved a joint developers' workshop and now the two CCPs are linking together with shared secretariat roles.

Highlights for the Current Reporting Period

Core highlights within the CCPForge software repository:-

  • Reconstruction Core algorithms: The optimisation of the iterative code for Diamond data sets is complete and has been tested on a sequence of reduced projection data from I13. Results look promising and the full sequence will be processed in 2015 Q1.The Windows GUI for lab based instruments has now been released to the wider community via a ccpforge download. This includes improved projection algorithms based on recent work by Will Thompson at Manchester. As a result a mode of the XTek instrument that is not currently supported has been identified. Support for this mode and other instruments is likely to be discussed at the next developers day.
  • Quantitative visualisation: Work on supporting the CCPi archive has continued and the current algorithms are available on multiple operating systems (Linux, Windows and Mac) and software products (Avizo, ParaView and ImageJ). Several new algorithms have been identified from the community that would be useful to include in the software repository and discussions held with the developers. A new implementation of a beam hardening correction algorithm (from Graham Davis) is currently being developed, in collaboration with users at RaCH and Leeds University. Another algorithm identified is measurement of tortuosity in 3D tube-like structure from Robert Bradley at MXIF and access to the source code is expected shortly. In collaboration with Diamond, a ParaView reader for NeXus data files has been developed and released.
  • Flagship project software outcomes: The non-local regularization package (patch-based method) for 2D/3D tomographic reconstruction is available on GPU and CPU. The modified version of the package has been used for improving spatial-temporal resolution of the simulated and real (neutron) data. Two novel methods available for multi-modal reconstruction, which can be useful for image fusion and also hybrid tomographic reconstruction, such as SPECT/CT, PET/MR etc. are being tested. The work continues on embedding the set of regularization tools (CPU and GPU versions) into the CCPi iterative reconstruction code.
  • A test tomography reconstruction and remote viewing system for the ISIS neutron spallation source has been complete and a set of evaluation code to create a service is currently being created. The service product is due for operation in April 2015.

An initial set of frameworks are being evaluated for inclusion within a future CCPi framework that will constitute a major part of the new CCPi; currently two; the Diamond Light Source savu framework; and the ISIS Neutron IMAT framework are being built for production service roles.

Outreach and networking:-

  • May 21, 2014 Celebration of The University of Manchester's Queen's Anniversary Prize for "New Techniques in X-ray Imaging of Materials Critical for Power, Transport and other Key Industries".
  • We manned a stand at the EuroVis (June 2014), hosted by Swansea University in the UK, the 16th annual visualization gathering organized by the Eurographics Working Group on Data Visualization and supported by the IEEE Visualization and Graphics Technical Committee (IEEE VGTC).
  • The annual Tomography for Scientific Advancement (ToScA) Symposium 1-3 September 2014, hosted at the Natural History Museum, London, UK had CCPi as a sponsor for the student poster competition as well as running a lively exhibition stand.
  • Workshops / Training; We continue to support training courses from the network: Includes, 1-2 December 2014 As part of the Diamond Manchester Collaboration, CCPi and HIP, the University of Manchester and Diamond Light Source ran a 2 day course on the Visualisation and quantification of tomographic data. The course was based around open-source software (ImageJ) and commercial software Avizo Software
  • The new series of social meetings at RAL (coffee-and-tomography) has hosted its 18th monthly meeting (total attendance now at 266). This has included in the last six months the first two recorded seminars, including the Pre-Christmas talk: by Prof Sarah Hainsworth, University of Leicester on "Forensic Applications of micro-computed tomography; Bones, flies and Richard III".
  • Developers’ workshop occur each quarter considering a specific focus; 22 October at QMUL related to overlap with PET / SPECT techniques; informal away-day on 22 July 2014 held at Nottingham's Hounsfield Facility; a multi-CT-machine with novel robotic-greenhouse attachment; and on 20 May held at Birmingham considering quantitative algorithms.

Flagship and publication activities: Related to the code integrated within the CCPForge, three papers have been accepted by Daniil Kazantsev including attendance at the Applied Inverse Problems conference, 2015 in Helsinki.; and the Royal Society Phil Trans A special edition now has a complete set of titles and authors (nine), with seven under peer review: Theme Issue is titled "X-ray Tomographic Reconstruction for Materials Science".

Widening participation: There has been through the RCaH a visiting fellow, Brian Bay, from LaVision Inc., who gave a tour: @ UCL then UoM and Oxford in July and August. The CCPi fellowship scheme also assisted in promoting the Drishti volume visualiser author Ajay Limaye, who on 8 September, gave a workshop and discussion of the features after a previous show and tell event at the NHM. Currently two members from the University of Bordeaux, Erwan Plougonven (Dec 2014) and Dominique Bernard (February 2015), are visiting the UK and exchanging experiences on source code integration for quantification visualisation (host is Ali Chirazi at University of Manchester).

EU involvement: There has been exchanges with the EU e-COST programme (EXTREME) with collaborating through workshops and conferences (links through Bill Lionheart, Mark Basham and Daniil Kazantsev). Events are proposed inviting the Astra software group to the UK and hosting a workshop or sponsored session during the 4D CT at the Applied Inverse Problems 2015 conference.

CCP Cross-collaborations:

  • CCP-ASEArch collaboration: Starting in April 2014 this work, by Evgueni Ovtchinnikov, involves numerical methods, to apply a multigrid solution to improve the issues caused by gradient based regularization coefficients in order to accelerate and stabilise convergence. This has now resulted in a publication to be submitted after collaboration with Daniil Kazantsev (CCPi Flagship Fellow).
  • The SLA EPSRC funded survey: the results for CCP visualisation user needs has been analysed to consider the long tail of products that the global community uses (>100 responses) and focus our CCPi core development effort on certain products.

Industrial Projects:

  • 30 June 2014 there was a TSB (UK Innovate) Kick-off meeting (project code 37972-241197) for an approved project within the Towards Zero Prototyping programme. Titled 'In silico evaluation of manufacturing concepts for non-Newtonian products' this collaborates with Prof Rob Prosser (University of Manchester), Drs Charles Moulinec and Rob Allan (STFC/SCD), Prof Adam Kowalski (Unilever) and CDDMtec aim to integrate computer CFD simulation, with tomographic 3D image capture; that will add the human-in-the-loop.

Workshops and New Opportunities

Future networking and sustainability opportunities include stronger links with industrial and laboratory based resources. This includes;

  • September 2015 ToScA Symposium number 3 will include further CCPi activities.
  • 30 June - 1 July 2015 EMiT held at University of Manchester: the EMiT (EMerging Technology) conference series brings together experts from all areas of computing to examine how to best take advantage of the changing landscape of computer hardware.
  • 9 March 2015 for three weeks, CLF Vulcan access for image acquisition
  • Continual links with the tomography standards panel (NPL/BSI cttee membership).

Training and developer's days are to continue as normal but other items also under consideration:

  • NVidia support through SCD has been offered and will be exploited in a forthcoming the developer’ workshops.
  • We are planning on an Avizo and ImageJ API multi-day workshop at Manchester in February involving developers and the software authors/owners to aid code integration;
  • A touchtable volume visualisation content creation day in April with four touchtables being commissioned or built across different CCPi partners.
  • A ParaView training day and software show-and-tell Kitware Inc (Marcus Hanwell) when author of TomView visits in September 2015
  • Funding to build a Rapiscan prototype tomography solution for Nicola Wadeson is agreed to come from the "Computer tomography CCP: widening participation" grant that has a few weeks left, and work is due to start in the next six months.

The CCPi has been in negotiations with a new CCP (MR/PET) and both proposals been successful for future funding in the next round of EPSRC networks. We are actively linking joint activities where appropriate for this new venture within the EPSRC SLA grant activities.

Issues and Problems

There is a still need to foster inter- and intra-networking between the two groups; the developers group and the user community. This requires improved communication across sites and involvement of remote participants. Increased levels of outreach as well as submitting proposal for increased resources; all are needed to gain a higher level of trust across the partners.

The next CCPi working group meeting is to be held in June 2015; where plans to create better collaboration and agreed focussed outcomes will be decided upon.

-- MartinTurner - 06 Jan 2015

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Topic revision: r6 - 09 Jan 2015 - MartinTurner
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