CCPi

Staffing: The project is proceeding as planned and now has a strong links with the core developer team (1.5 FTE); Barry Searle (based at DL), and Srikanth Nagella and Ronald Fowler (based at RAL). Over the last year due to an underspend we have had extra resources (total 0.45 FTE) for 0.2 FTE Martin Turner for secretariat roles and 0.25 FTE Erica Yang for tomographic links with the ISIS (Neutron spallation source) IMAT beamline.

Administration: Regular working group meetings were organised during Q2 and Q4 of 2014; a series of developers workshop have continued on a quarterly basis: 14 Jan 2014 and 20 May 2014 in Birmingham; 22 July 2014 at Nottingham and 22 October 2014 in QMUL; and we also assisted and presented in the second Tomography for Scientific Advancement symposium (ToScA) in the Natural History Museum (1-3 Sep 2014) involving a stand and keynote talks. The extra monthly showcase meetings involving software show-and-tells is organised at RAL and has continued with 18 events in the series (total attendance 290); including at the end of 2014 two recorded sessions (56 external views). There have been an exhibition stands and presence at various events including in Q1 2015 the first touchtable activity point.

Collaboration: After a CCPi Seminar in Nov 2013, work started with CCP-ASEArch in April 2014 by Evgueni Ovtchinnikov; involving 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). With the ISIS Neutron Spallation source we have put together a package with an extra 2.0 FTE to create a new tomographic framework for the IMAT beamline due to be in operation as a service in Q2 2015 (Initiall tests complete in Q4 2014). With Diamond Light Source we are assisting in constructing their new framework "Savu" that is under test Q1 2015, and due for release in Q3 2015. A third framework is collaborating with lab based suppliers, focussing ion Nikon Metrology machines is commencing Q1 2015.

These collaborations have brought in extra effort and may incur a slight SLA underspend to carry over to the remainder of the CCPi first phase to complete by 28 August 2015 (about 2.5 man months).

We have agreed future collaborations with Rapiscan Inc. involving a short project (3 months) to apply reconstruction codes for a new security scanning system (involving Nicola Wadeson); Daniil Kazantsev is retained to continue to end of phase 1; 28 August 2015 in core activities of code porting to the CCPForge; a short visualisation tomography project linking to CFD simulation is agree with (TSB) UK Innovation with Unilever for 4 months, and proposals are in with ISIS to continue the new reconstruction framework.

Publications: Related to the code integrated, with the flagship project, 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 papers), with seven currently under peer review: Theme Issue is titled "X-ray Tomographic Reconstruction for Materials Science".

Training etc: A series of courses have been coordinated and software supported; including licenses servers, have assisted with the Diamond Light Source, Research Compex at Harwell and University of Manchester: four multi-day courses held annualy at RAL and four multi-day courses held at Manchester and two specialist courses at SCD/STFC: including a Christmas lecture.

Development targets met in year for CCPi up to January 2015:

  • The exisiting quantification algorithms have all been revised into more portable formats. This has allowed them to be made available in the three choosen packages (Avizo, ImageJ and ParaView) with a common source code base to improve maintainability.
  • The accessible volume algorithm has been improved and tested. It is now scales well to large image size.
  • Initial particle tracking code based on MXIF is complete with modifications now made to determine proximity of particles from one form to the next.
  • The histogram based thresholding methods has been implemented with extended versions planned (quanification developer's workshop Feb 17-20 2015).
  • Work on a generalised implementation of a beam hardening algorithm is in progress in collaboration with Graham Davis (QMUL) and RaCH staff.
  • Iterative reconstruction development proceeds; a NeXus? reader for Diamond Light Source data sets is written and deployed; integrated with a CGLS code.
  • Test runs on Hartee systems for iterative methods continue but can require about 20hrs/iteration. The code has been modified to reduce memory requirements for workstations and the next stage is looking at alternative technologies.
  • A dedicated CCPi YouTube? channel continues to be exploited:http://www.youtube.com/channel/UCGB578xcyXNQyiBsufEFIeQ
  • Added two new iterative reconstruction algorithms from network members and flagship project and on the CCPForge.

Metrics for 2014/5

Highlights during the financial year 2014/5:

  • STFC staff have been no direct publications but a set of papers are in preparation
  • STFC staff have given some 7 presentations at meetings ranging from formal site visits (four developers' day site visit presentations) to three invited talks at conferences and exhibition meetings (including KTN etc).
  • There has been one main publication (Daniil Kazantsev et al 2014 Inverse Problems 30 065004. doi:10.1088/0266-5611/30/6/065004) that reference codes developed through the SLA and others in press
  • Over 10 training courses there were 18 training days covering PhD supervision, code workshops and scientific meetings. Average attendance was 12 and approximately a quarter were directly of indirectly PhD students (approx 54 PhD student days of training).

April 2014 - March 2015



Technical Appendix plans for 2015

CCPi – Tomographic Imaging - and CCP PET/MR - positron emission tomography and magnetic resonance imaging

Non destructive 3D X-ray, Neutron, PET and MR imaging are becoming increasingly important in many areas of science with application to Energy, Healthcare and Security. For example X-rays are having a dramatic impact on fields as diverse as security (e.g. baggage and body scanning at airports and screening of vehicles at ports), engineering (e.g. visualising stress corrosion cracking in nuclear plant and the degradation of fuel cells) and medicine (e.g. cancer treatment and artificial tissue engineering). The spatial and temporal resolutions are increasing dramatically. RC funded synchrotron sources are rapidly increasing the numbers of x-ray imaging instruments available (the European Synchrotron Radiation Facility (ESRF) now has 10 beamlines, Diamond Light Source (DLS) is currently building 4 new imaging beamlines). Laboratory x-ray imaging facilities are becoming increasingly widespread. This expansion is mirrored elsewhere with the global CT market now worth $150M (+ $5B in medical CT) both expanding at 10% pa , while 30% of the data stored on the world's computers are now medical images. Unsurprisingly, papers on x-ray tomography have also increased sharply this decade.

These two CCPs aim to provide a toolbox of algorithms that increase the quality and level of information that can be extracted from computer tomography. The CCPs will bring together the imaging community, maximise return on investment in software development and ensure longevity, sustainability and re-use of code.

Outline of Proposed Core Support Activities:

Most people who acquire and analyse images have little or no knowledge of the type of tomography reconstruction or analysis available; consequently the involvement of the Core Support is critical to achieve a significant step jump in the level of information obtained by UK science from X-ray and PET imaging. As well as administrative support for all of the CCPs (organization of working group meetings, maintenance of web sites), the core support team (1.25 FTE per annum per CCP) will:

  • Standardise input and output data formats;
  • Standardise software coding rules and testing;
  • Assist with porting, parallelisation and optimisation on different hardware platforms including novel architecture systems.
  • Provide centralised distribution and controlled releases for software;
  • Provide installation user support for software, and run workshops/training events;
  • Collate and distribute existing algorithms and code, including licensing requests;
  • Encourage CCPs participants to make their algorithms and code available;
  • Create a gallery of test real image and volume datasets for mathematicians to test and benchmark new algorithms; and
  • Maintain documentation.

For CCPi: This project aims to provide toolboxes for both 3D image reconstruction and 3D image analysis algorithms. In simple terms it is estimated that the project requires 0.2 FTE for maintaining network, website, running workshops and training course, benchmarking, licensing issues etc; 0.3 FTE enhancing a framework, 0.3FTE for developing and maintaining the 3D image analysis toolbox, 0.3FTE for developing and maintaining the image reconstruction toolbox.

For CCP PET/MR: This project aims initially to improve the current coding source forge archive, including profiling, benchmarking for new architectures, as well as seting up a framework including new test data sets (1.1FTE).

A long term milestone, for end of 2016, for both CCPs is to do true time based iterative versions of the code that are agreed and used by the community on real data (up to 2000^4).

CCPi Milestone Date: transfer from first phase to second phase is 28 August 2015

  • Website, mailing lists, source code archives - Ongoing
  • Organise working group meeting/ ToScA involvement, and monthly joint show-and-tell sessions - Ongoing
  • Support current training courses and organise developer workshop to teach (for C++ includes; Basics of an application (Avizo, ImageJ); Programming (C++/Java) with reference to particular API; API for Avizo, VolView, ImageJ; Development with ITK; Implement a module to take away) - Liase with software carpentry courses and training with the CCPForge. Ongoing
  • Develop framework analysis for national facilities: DLS "Savu" and IMAT (ISIS) Q2 2015 release - then ongoing with lab based framework.
  • Iterative code Framework for lab based Nikon Metrology XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work that can tackle problems with fewer images. Q3 2015 - framework review end of phase (28 Aug 2015)
  • Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in !VolView and Avizo. To be rereleased after publication Q3 2015
  • Beam hardening correction code (from QMUL) to be completed and tested. Results to be published end of phase (28 Aug 2015).
  • Implementation of further quantification algorithms for and from the community (Extra; potential to support Avizo, !ImageJ and !ParaView) - Q2 2015
  • Capture multiple idealised datasets - initial data in unstored form completed in Q4 2014 (Birmingham data), continuing Q2 2015 with DOI entries (Manchester and Southampton data)
  • OpenCL accelerated version of forward and backward projectors for iterative reconstruction algorithms - Q4 2015
  • Flagship: Integration of (at least) CPU-based iterative algorithms from flagship grant into Matlab independent code - Q3 2015
  • Optional post Q4 2015: Iterative code for the Nikon XTek X-Ray CT Already released - Now that the CPU versions of the reconstruction are under control - accelerated versions (OpenCL, Xeon Phi).
  • Optional post Q4 2015: Integration of iterative algorithms into the DLS "Savu" framework.
  • Optional post Q4 2015: Optimise OpenCL projection algorithms

CCP_PET/MR Milestone Dates: Draft as under negotiations when Working Group form in 1 April 2014

  • Establish website, mailing lists, source code archives -Ongoing
  • Organise working group meeting/ user-conference involvement, and monthly joint show-and-tell sessions - Ongoing
  • Support current training courses and organise developer workshop (C++, SWIG to interface to matlab and python, git) - Q3 2015
  • Establish database for both simulated and acquired data (i.e. set-up of framework, will slowly be filled over the project) - Q4 2015
  • Visit sites in the network to gain experience with a few selected packages for image reconstruction - one key site per Quarter
  • Support benchmarking and testing of a few selected packages - Q4 2015
  • Creation and maintenance of test-cases of PET/MR data and reconstructions - Q4 2015 and release Q1 2016
  • Profiling and (if necessary initial speed-up) of 1 PET and 1 MR image reconstruction package - Q3 2015 and Q1 2016

Task Effort 2015-2016

  • Secretariat Coordination for both CCPs 0.15
  • Basic maintaining network, website, organising administration for workshops and training courses, (Core SLA activities allocation) 0.175
  • Benchmarking, profiling, licensing issues 0.685
  • CCPi Framework Developing and maintaining the 3D image analysis toolbox; noise preprocessing, reconstruction and qpost-quantification 0.80
  • CCP_PET/MR Developing and maintaining the image reconstruction toolbox 0.80

Total 2.6 FTEs

Staffing Effort 2015-2016 - Out of Date now

  • Group Leader - Martin Turner 0.465
  • Barry Searle 0.17
  • Srikanth Nagella 0.69
  • Ron Fowler 0.26
  • "AN Other" 0.84
  • Returned allocation to Core SLA activities website etc. 0.175

Total 2.6 FTEs

-- MartinTurner - Feb 2015

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