Difference: SLACombinedReport (8 vs. 9)

Revision 927 Jan 2015 - MartinTurner

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META TOPICPARENT name="CCPiTomo"
CCPi
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  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.
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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 "Sabu" that is under test Q1 2015, and due for release in Q3 2015.
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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 "Sabu" 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".
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 Highlights during the financial year 2013/4:

  • STFC staff have produced some xxx publications not including papers in preparation
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  • STFC staff have given some 7 presentations at meetings ranging from informal site visits (four developers' day site visit presentations) to invited talks at major conferences and three exhibition (KTN) meetings.
  • There are three publications that reference codes developed through the SLA
  • Some 33 training days covering PhD supervision, code workshops and scientific meetings. xx were for PhD students.
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  • STFC staff have given some 7 presentations at meetings ranging from informal site visits (four developers' day site visit presentations) to invited talks at conferences and three exhibition (KTN) meetings.
  • There are 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 two in press plus special issue on Phil Trans.
  • Some 33 training days covering PhD supervision, code workshops and scientific meetings. xx were for PhD students.
  STILL need some metrics for CCPi.
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  CCPi – Tomographic Imaging - and CCP PET/MR - positron emission tomography and magnetic resonance imaging
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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 (doubling every 3 years with 1,500 published last year).
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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.
 
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These CCPs aims 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.
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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:
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  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).
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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

  • 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
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  • Develop framework analysis for national facilities: DLS "Savu" and IMAT (ISIS) Q2 2015 release - then ongoing
  • 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 Q4 2015
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  • Develop framework analysis for national facilities: DLS "Sabu" 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
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  • Beam hardening correction code to be completed and tested. Results to be published.
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  • 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
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  • Capture multiple idealised datasets - initial data in unstored form completed in Q4 2014 (Birmingham data), continuing Q2 2015 (Manchester and Southampton data)
  • 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) should be on the 2015 plan.
  • OpenCL accelerated version of forward and backward projectors for iterative reconstruction algorithms - Q2 2015
  • Integration of (at least) CPU-based iterative algorithms from flagship grant into Matlab independent code - Q3 2015
  • Optional: Integration of iterative algorithms into the DLS "Savu" framework.
  • Optional: Optimise projection algorithm at the core of iterative routines for an accelerated architecture (GPU/Phi).
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  • 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 "Sabu" framework.
  • Optional post Q4 2015: Optimise projection algorithm at the core of iterative routines for an accelerated architecture (GPU/Phi).
  CCP_PET/MR Milestone Dates
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  Total 2.5 FTEs
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-- MartinTurner - 09 Jan 2015
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-- MartinTurner - 27 Jan 2015
 
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