Difference: SLACombinedReport (1 vs. 14)

Revision 1404 Mar 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="CCPiTomo"
CCPi
Line: 99 to 99
  Task Effort 2015-2016
Changed:
<
<
  • Secretariat Coordination for both CCPs 0.2
  • Basic maintaining network, website, organising administration for workshops and training courses, (Core SLA activities allocation) 0.14
  • Benchmarking, profiling, licensing issues 0.66
>
>
  • 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

Changed:
<
<
Staffing Effort 2015-2016
>
>
Staffing Effort 2015-2016 - Out of Date now
 
Changed:
<
<
  • Group Leader - Martin Turner 0.50
>
>
  • Group Leader - Martin Turner 0.465
 
  • Barry Searle 0.17
  • Srikanth Nagella 0.69
  • Ron Fowler 0.26
  • "AN Other" 0.84
Changed:
<
<
  • Returned allocation to Core SLA activities website etc. 0.14
>
>
  • Returned allocation to Core SLA activities website etc. 0.175
  Total 2.6 FTEs
Changed:
<
<
-- MartinTurner - 27 Jan 2015
>
>
-- MartinTurner - Feb 2015
 \ No newline at end of file

Revision 1328 Jan 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="CCPiTomo"
CCPi
Line: 27 to 27
 
  • 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.
Changed:
<
<

Metrics 2013/4 need values for 2014/5

>
>

Metrics for 2014/5

 
Changed:
<
<
Highlights during the financial year 2013/4:
>
>
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).
Changed:
<
<
  • 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 two in press plus special issue on Phil Trans.
  • Over 10 training courses there were 33 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 100 PhD student days of training).
>
>
  • 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
Line: 97 to 97
 
  • 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
Changed:
<
<
Task Effort
>
>
Task Effort 2015-2016
 
  • Secretariat Coordination for both CCPs 0.2
  • Basic maintaining network, website, organising administration for workshops and training courses, (Core SLA activities allocation) 0.14
Line: 107 to 107
  Total 2.6 FTEs
Changed:
<
<
Staffing Effort
>
>
Staffing Effort 2015-2016
 
  • Group Leader - Martin Turner 0.50
  • Barry Searle 0.17

Revision 1228 Jan 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="CCPiTomo"
CCPi
Line: 69 to 69
  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).
Changed:
<
<
CCPi Milestone Date
>
>
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
Line: 86 to 86
 
  • Optional post Q4 2015: Integration of iterative algorithms into the DLS "Savu" framework.
  • Optional post Q4 2015: Optimise OpenCL projection algorithms
Changed:
<
<
CCP_PET/MR Milestone Dates: Draft as under negotiations when Working Group form in April 2014
>
>
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
Line: 100 to 100
 Task Effort

  • Secretariat Coordination for both CCPs 0.2
Changed:
<
<
  • Basic maintaining network, website, organising administration for workshops and training courses, (Core SLA activities allocation) 0.175
  • Benchmarking, profiling, licensing issues 0.525
  • CCPi Framework Developing and maintaining the 3D image analysis toolbox; noise preprocessing, reconstruction and qpost-quantification 0.8
  • CCP_PET/MR Developing and maintaining the image reconstruction toolbox 0.8
>
>
  • Basic maintaining network, website, organising administration for workshops and training courses, (Core SLA activities allocation) 0.14
  • Benchmarking, profiling, licensing issues 0.66
  • 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
 
Changed:
<
<
Total 2.5 FTEs
>
>
Total 2.6 FTEs
  Staffing Effort
Changed:
<
<
  • Group Leader - Martin Turner 0.2+0.4
>
>
  • Group Leader - Martin Turner 0.50
 
  • Barry Searle 0.17
Changed:
<
<
  • Srikanth Nagella 0.61
  • Ron Fowler 0.22
>
>
  • Srikanth Nagella 0.69
  • Ron Fowler 0.26
 
  • "AN Other" 0.84
Changed:
<
<
  • Returned allocation to Core SLA activities website etc. 0.175
>
>
  • Returned allocation to Core SLA activities website etc. 0.14
 
Changed:
<
<
Total 2.5 FTEs
>
>
Total 2.6 FTEs
  -- MartinTurner - 27 Jan 2015

Revision 1127 Jan 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="CCPiTomo"
CCPi
Line: 14 to 14
  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".
Changed:
<
<
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 a specialist annual course at SCD/STFC: including a Christmas lecture.
>
>
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:
Line: 22 to 22
 
  • 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).
Changed:
<
<
  • 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.
>
>
  • 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.
Changed:
<
<
  • A dedicated CCPi YouTube? channel continues to be exploited:http://www.youtube.com/channel/UCGB578xcyXNQyiBsufEFIeQ
>
>
  • 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 2013/4 need values for 2014/5

Highlights during the financial year 2013/4:

Changed:
<
<
  • STFC staff have produced some xxx publications not including papers in preparation
  • 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.

>
>
  • 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 two in press plus special issue on Phil Trans.
  • Over 10 training courses there were 33 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 100 PhD student days of training).
  April 2014 - March 2015
Line: 76 to 74
 
  • 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
Changed:
<
<
  • Develop framework analysis for national facilities: DLS "Sabu" and IMAT (ISIS) Q2 2015 release - then ongoing with lab based framework.
>
>
  • 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).
Line: 85 to 83
 
  • 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).
Changed:
<
<
  • 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).
>
>
  • Optional post Q4 2015: Integration of iterative algorithms into the DLS "Savu" framework.
  • Optional post Q4 2015: Optimise OpenCL projection algorithms
 
Changed:
<
<
CCP_PET/MR Milestone Dates
>
>
CCP_PET/MR Milestone Dates: Draft as under negotiations when Working Group form in 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
Line: 101 to 99
  Task Effort
Changed:
<
<
  • Secretariat Coordination 0.2
>
>
  • Secretariat Coordination for both CCPs 0.2
 
  • Basic maintaining network, website, organising administration for workshops and training courses, (Core SLA activities allocation) 0.175
  • Benchmarking, profiling, licensing issues 0.525
  • CCPi Framework Developing and maintaining the 3D image analysis toolbox; noise preprocessing, reconstruction and qpost-quantification 0.8

Revision 1027 Jan 2015 - SriNagella

Line: 1 to 1
 
META TOPICPARENT name="CCPiTomo"
CCPi
Line: 6 to 6
  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.
Changed:
<
<
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.
>
>
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).

Revision 927 Jan 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="CCPiTomo"
CCPi
Line: 6 to 6
  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.
Changed:
<
<
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.
>
>
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".
Line: 28 to 32
 Highlights during the financial year 2013/4:

  • STFC staff have produced some xxx publications not including papers in preparation
Changed:
<
<
  • 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.
>
>
  • 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.
Line: 43 to 47
  CCPi – Tomographic Imaging - and CCP PET/MR - positron emission tomography and magnetic resonance imaging
Changed:
<
<
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).
>
>
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.
 
Changed:
<
<
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.
>
>
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:
Line: 65 to 69
  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).
Added:
>
>
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
Changed:
<
<
  • 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
>
>
  • 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
Changed:
<
<
  • Beam hardening correction code to be completed and tested. Results to be published.
>
>
  • 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
Changed:
<
<
  • 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).
>
>
  • 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
Line: 114 to 120
  Total 2.5 FTEs
Deleted:
<
<
-- MartinTurner - 09 Jan 2015
 \ No newline at end of file
Added:
>
>
-- MartinTurner - 27 Jan 2015

Revision 827 Jan 2015 - RonFowler

Line: 1 to 1
 
META TOPICPARENT name="CCPiTomo"
CCPi
Line: 73 to 73
 
  • 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
  • Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in !VolView and Avizo. To be rereleased after publication Q3 2015
Added:
>
>
  • Beam hardening correction code to be completed and tested. Results to be published.
 
  • 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 (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.

Revision 727 Jan 2015 - RonFowler

Line: 1 to 1
 
META TOPICPARENT name="CCPiTomo"
CCPi
Line: 6 to 6
  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.
Changed:
<
<
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 opperation as a service in Q2 2015 (Inialial tests complete in Q4 2014). With Diaminad Light Source we are assisting in constructing their new framework "Sabu" that is under test Q1 2015, and due for release in Q3 2015.
>
>
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.
  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".
Changed:
<
<
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-daty courses held at Manchester and a specialist annual course at SCD/STFC: including a Christmas lecture.
>
>
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 a specialist annual course at SCD/STFC: including a Christmas lecture.
  Development targets met in year for CCPi up to January 2015:
Added:
>
>
  • 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.
Changed:
<
<
  • The histogram based thresholding methods has been implemented with extended versions planned for 2015 involving a four day developer's intense session (confirnmed Feb 17-20 2015).
>
>
  • 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

Revision 626 Jan 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="CCPiTomo"
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.

Changed:
<
<
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 (48 external views). There have been an exhibition stands and presence at various events including in Q1 2015 the first touchtable activity point.
>
>
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 opperation as a service in Q2 2015 (Inialial tests complete in Q4 2014). With Diaminad Light Source we are assisting in constructing their new framework "Sabu" that is under test Q1 2015, and due for release in Q3 2015.
Line: 17 to 17
 
  • 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 for 2015 involving a four day developer's intense session (confirnmed Feb 17-20 2015).
  • Iterative reconstruction development proceeds; a NeXus? reader for Diamond Light Source data sets is written and deployed; integrated with a CGLS code.
Changed:
<
<
  • Test runs on Hartee systems for iterative methods continue and require about about 20hrs/iteration. The code has been modified to reduce memory requirements for workstations and the next stage is looking at alternative technologies.
>
>
  • 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 2013/4 need values for 2014/5

Changed:
<
<
Highlighta during the financial year 2013/4:
>
>
Highlights during the financial year 2013/4:
 
  • STFC staff have produced some xxx publications not including papers in preparation
Changed:
<
<
  • STFC staff have given some 7 presentations at meetings ranging from informal site visits (three developers' site visits pres.) to invited talks at major conferences and three exhibition (KTN) meetings.
  • There are some xxx 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.
>
>
  • 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.
  STILL need some metrics for CCPi.
Line: 60 to 60
  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.
Changed:
<
<
For CCP PET/MR: This project aims to improve the current coding source forge archive, includeing profiling, benchmarking for new architectures, as well as seting up a framework including new test data sets (1.1FTE).
>
>
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).
  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
Changed:
<
<
  • Develop framework analyssis: DAWN sabu and IMAT (ISIS) Q2 2015 releadse - then ongoing
  • Iterative code Framework for Nikon XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work - can tackle problems with fewer images. Q3 2015 - framework review Q4 2015
  • Update
  • Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in !VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3 - Q3 2014
  • Implementation of two/three further quantification algorithms for and from the community (Extra; potential to support Avizo, !ImageJ and !ParaView) - Q3 2014
>
>
  • 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
  • Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in !VolView and Avizo. To be rereleased after publication Q3 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 (Manchester and Southampton data)
Changed:
<
<
  • Iterative code for the Nikon XTek X-Ray CT Released Q1 2015 - Now that the CPU versions of the reconstruction are under control - accelerated versions (OpenCL, Xeon Phi) should be on the 2015 plan.
>
>
  • 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
Changed:
<
<
  • Integration of iterative algorithms into DLS SAVU framework - ongoing.
  • Optional: Optimise projection algorithm at the core of iterative routines for an accelerated architecture (GPU/Phi) Q1 2014. The optimised Diamond version has been tested on Xeon Phi and further work tests will occur as part of the ongoing optimisation.
>
>
  • 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).
  CCP_PET/MR Milestone Dates

Revision 526 Jan 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="CCPiTomo"
CCPi
Changed:
<
<
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 for 0.2 FTE Martin Turner for secretariat roles and 0.45 FTE Erica Yang for tomographic links with the ISIS (Neutron spallation source) IMAT beamline.
>
>
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.
 
Changed:
<
<
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 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 (48 external views).
>
>
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 (48 external views). There have been an exhibition stands and presence at various events including in Q1 2015 the first touchtable activity point.
 
Changed:
<
<
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 ftanework for the IAMT beamline due to be in opperation as a service in Q2 2015.
>
>
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 opperation as a service in Q2 2015 (Inialial tests complete in Q4 2014). With Diaminad Light Source we are assisting in constructing their new framework "Sabu" that is under test Q1 2015, and due for release in Q3 2015.
  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".
Changed:
<
<
Training etc: A series of courses have been coordinated and software support, including licenses servers, have assisted the Diamond Light Source, Research Compex at Harwell and University of Manchester.
>
>
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-daty courses held at Manchester and a specialist annual course at SCD/STFC: including a Christmas lecture.
  Development targets met in year for CCPi up to January 2015:

  • Initial particle tracking code based on MXIF is complete with modifications now made to determine proximity of particles from one form to the next.
Changed:
<
<
  • The histogram based thresholding methods has been implemented with extended versions planned for 2015.
>
>
  • The histogram based thresholding methods has been implemented with extended versions planned for 2015 involving a four day developer's intense session (confirnmed Feb 17-20 2015).
 
  • 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 and require about 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 2013/4 need values for 2014/5

Changed:
<
<
FOR ALL CCPs. We would highlight that during the financial year 2013/4 (figures from last year’s report in brackets):
>
>
Highlighta during the financial year 2013/4:
 
  • STFC staff have produced some xxx publications not including papers in preparation
Changed:
<
<
  • STFC staff have given some xxx presentations at meetings ranging from informal site visits to invited talks at major conferences.
>
>
  • STFC staff have given some 7 presentations at meetings ranging from informal site visits (three developers' site visits pres.) to invited talks at major conferences and three exhibition (KTN) meetings.
 
  • There are some xxx publications that reference codes developed through the SLA
Changed:
<
<
  • Some xxx training days covering !PhD supervision, code workshops and scientific meetings.
>
>
  • Some 33 training days covering !PhD supervision, code workshops and scientific meetings. xx were for PhD students.
 
Changed:
<
<
NEED metrics for CCPi.
>
>
STILL need some metrics for CCPi.
  April 2014 - March 2015
Line: 58 to 58
 
  • Create a gallery of test real image and volume datasets for mathematicians to test and benchmark new algorithms; and
  • Maintain documentation.
Changed:
<
<
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 0.3FTE for maintaining network, website, running workshops and training course, benchmarking, licensing issues etc; 0.5FTE for developing and maintaining the 3D image analysis toolbox, 0.5FTE for developing and maintaining the image reconstruction toolbox.
>
>
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.
 
Changed:
<
<
For CCP PET/MR: This project aims to improve the current coding source forge archive, includeing profiling, benchmarking for new architectures, as well as seting up a framework including new test data sets.
>
>
For CCP PET/MR: This project aims to improve the current coding source forge archive, includeing profiling, benchmarking for new architectures, as well as seting up a framework including new test data sets (1.1FTE).
  CCPi Milestone Date
Changed:
<
<
  • Organise working group meeting/ ToScA involvement, and monthly 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.
  • Port 3 or 4 iterative codes so that they can be compared on the same datasets
  • Tidy up of centre of rotation issues and optimisation of iterative code with Diamond NeXuS data sets for integration with DAWN. Q4 2014 and 3.2; Port of Manchester filtered back projection into NeXuS? package as an option with DAWN - Q1 2015) Q4 2014
  • Iterative code up and working for the Nikon XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work - can tackle problems with fewer images.
  • Work with Tristan Lowe in Manchester to define a beta version (in the ccpforge) - (Release data release version Q1 2015) Q2 2014
>
>
  • 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 analyssis: DAWN sabu and IMAT (ISIS) Q2 2015 releadse - then ongoing
  • Iterative code Framework for Nikon XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work - can tackle problems with fewer images. Q3 2015 - framework review Q4 2015
  • Update
 
  • Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in !VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3 - Q3 2014
  • Implementation of two/three further quantification algorithms for and from the community (Extra; potential to support Avizo, !ImageJ and !ParaView) - Q3 2014
Changed:
<
<
  • Capture multiple idealised datasets - initial version has a minimum of 2048 images each comprising 8 frames so that we could for example compare reconstructing 2048 1 frame projections with 1024 (each 2 frames summed) projections with 512 (each 4 frames summed) projections with 256 (each 8 frames summed) projections [with Diamond (Mark Bashham) - Q4 2014] conting Q2 2015
>
>
  • 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 Released Q1 2015 - Now that the CPU versions of the reconstruction are under control - accelerated versions (OpenCL, Xeon Phi) should be on the 2015 plan.
Changed:
<
<
  • DAWN integration is on this 2014 plan but will be ongoing.
  • Optimise projection algorithm at the core of iterative routines for an accelerated architecture (GPU/Phi) Q1 2014. The optimised Diamond version has been tested on Xeon Phi and further work tests will occur as part of the ongoing optimisation.
>
>
  • 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
  • Integration of iterative algorithms into DLS SAVU framework - ongoing.
  • Optional: Optimise projection algorithm at the core of iterative routines for an accelerated architecture (GPU/Phi) Q1 2014. The optimised Diamond version has been tested on Xeon Phi and further work tests will occur as part of the ongoing optimisation.
  CCP_PET/MR Milestone Dates
Changed:
<
<
  • Establish website, mailing lists, source code archives
  • Establish database for both simulated and acquired data (i.e. set-up of framework, will slowly be filled over the project)
  • Organise working group meeting involvement, and monthly show-and-tell sessions
  • Support current training courses and organise developer workshop (C++, SWIG to interface to matlab and python, git)
  • Visit sites in the network to gain experience with a few selected packages for image reconstruction.
  • Support benchmarking and testing of a few selected packages
  • Creation and maintenance of test-cases of PET/MR data and reconstructions
  • Profiling and (if necessary initial speed-up) of 1 PET and 1 MR image reconstruction package
>
>
  • 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

  • Secretariat Coordination 0.2
Changed:
<
<
  • Basic maintaining network, website, organising administration for workshops and training courses, 0.175
>
>
  • Basic maintaining network, website, organising administration for workshops and training courses, (Core SLA activities allocation) 0.175
 
  • Benchmarking, profiling, licensing issues 0.525
  • CCPi Framework Developing and maintaining the 3D image analysis toolbox; noise preprocessing, reconstruction and qpost-quantification 0.8
  • CCP_PET/MR Developing and maintaining the image reconstruction toolbox 0.8
Line: 100 to 102
  Staffing Effort
Changed:
<
<
  • Martin Turner 0.2
  • Barry Searle 0.5
  • Srikanth Nagella 0.5
  • Ron Fowler 0.325
  • Ron Hate 0.8
  • Returned to Core SLA activities website etc. 0.175
>
>
  • Group Leader - Martin Turner 0.2+0.4
  • Barry Searle 0.17
  • Srikanth Nagella 0.61
  • Ron Fowler 0.22
  • "AN Other" 0.84
  • Returned allocation to Core SLA activities website etc. 0.175
  Total 2.5 FTEs

Revision 412 Jan 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="CCPiTomo"
CCPi
Changed:
<
<
Staffing: The project is proceeding as planned and now has a strong links with the core developers; 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 resources for 0.2 FTE Martin Turner for extra secretariate roles and 0.45 FTE Erica Yang for tomographic links with the ISIS (Neutron spallation source) IMAT beamline.
>
>
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 for 0.2 FTE Martin Turner for secretariat roles and 0.45 FTE Erica Yang for tomographic links with the ISIS (Neutron spallation source) IMAT beamline.
 
Changed:
<
<
Administration: Working group meetings were organised during Q2 and Q4 of 2014; a series of developers workshop have continues on a quarterly basis: 14 Jan 2014 and 20May 2014 in Birmingham; 22 July 2014 at Nottingham and 22 October 2014 in QMUL; and we also assisted 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 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 (48 external views).
>
>
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 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 (48 external views).
 
Changed:
<
<
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).
>
>
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 ftanework for the IAMT beamline due to be in opperation as a service in Q2 2015.
  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 support, including licenses servers, have assisted the Diamond Light Source, Research Compex at Harwell and University of Manchester.

Changed:
<
<
Development targets met for CCPi up to January 2015:
>
>
Development targets met in year for CCPi up to January 2015:
 
  • Initial particle tracking code based on MXIF is complete with modifications now made to determine proximity of particles from one form to the next.
Changed:
<
<
  • The histogram based thresholding methods is implemented with extended versions planned for 2015.
  • Iterative reconstruction development proceeds; a NeXus? reader for Diamond Light Source data sets is written and deployed; integrated with a CGLS code to analyse Diamond data sets.
  • Test runs on Hartee systems for iterative methods continue and require about about 20hrs/iteration. The code has been modified to reduce memory requirements for workstations and next stage is looking at alternative technologies.
>
>
  • The histogram based thresholding methods has been implemented with extended versions planned for 2015.
  • 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 and require about 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
Changed:
<
<
  • Optimise projection algorithm at the core of iterative routines for an accelerated architecture (GPU/Phi) Q1 2014. The optimised Diamond version has been tested on Xeon Phi and further work tests will occur as part of the ongoing optimisation.
  • Added two new iterative reconstruction algorithms from network members and flagship project and on the CCPForge.
>
>
  • Added two new iterative reconstruction algorithms from network members and flagship project and on the CCPForge.
 

Metrics 2013/4 need values for 2014/5

FOR ALL CCPs. We would highlight that during the financial year 2013/4 (figures from last year’s report in brackets):

Changed:
<
<
  • STFC staff have produced some 51 (107) publications not including papers in preparation
  • STFC staff have given some 101 (109) presentations at meetings ranging from informal site visits to invited talks at major conferences.
  • There are some 1629 (1497) publications that reference codes developed through the SLA
  • Some 4451 (3732) training days covering !PhD supervision, code workshops and scientific meetings.
>
>
  • STFC staff have produced some xxx publications not including papers in preparation
  • STFC staff have given some xxx presentations at meetings ranging from informal site visits to invited talks at major conferences.
  • There are some xxx publications that reference codes developed through the SLA
  • Some xxx training days covering !PhD supervision, code workshops and scientific meetings.
  NEED metrics for CCPi.
Line: 39 to 38
 

Technical Appendix plans for 2015

Changed:
<
<
CCPi – Tomographic Imaging - and CCP pet/mr
>
>
CCPi – Tomographic Imaging - and CCP PET/MR - positron emission tomography and magnetic resonance imaging
 
Changed:
<
<
Non destructive 3D X-ray, Neutron, PET and MR imaging is 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).
>
>
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).
  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.

Outline of Proposed Core Support Activities:

Changed:
<
<
Most people who acquire and analyse images have little or no knowledge of the type of tomography reconstruction or analysis; consequently the involvement of the Core Support is critical if we are 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:
>
>
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;
Line: 59 to 58
 
  • Create a gallery of test real image and volume datasets for mathematicians to test and benchmark new algorithms; and
  • Maintain documentation.
Changed:
<
<
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 0.5FTE for maintaining network, website, running workshops and training course, benchmarking, licensing issues etc; 0.5FTE for developing and maintaining the 3D image analysis toolbox, 0.5FTE for developing and maintaining the image reconstruction toolbox.
>
>
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 0.3FTE for maintaining network, website, running workshops and training course, benchmarking, licensing issues etc; 0.5FTE for developing and maintaining the 3D image analysis toolbox, 0.5FTE for developing and maintaining the image reconstruction toolbox.
 
Changed:
<
<
For CCP pet/mr: this project ...
>
>
For CCP PET/MR: This project aims to improve the current coding source forge archive, includeing profiling, benchmarking for new architectures, as well as seting up a framework including new test data sets.
  CCPi Milestone Date
Changed:
<
<
  • 1 Organise working group meeting/ ToScA involvement, and monthly show-and-tell sessions - Ongoing
  • 2. 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) - Q4 2014
>
>
  • Organise working group meeting/ ToScA involvement, and monthly 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.
 
  • Port 3 or 4 iterative codes so that they can be compared on the same datasets
Changed:
<
<
  • Extra targets: 3.1 Tidy up of centre of rotation issues and optimisation of iterative code with Diamond NeXuS data sets for integration with DAWN. Q4 2014 and 3.2; Port of Manchester filtered back projection into NeXuS? package as an option with DAWN - Q1 2015) Q4 2014
>
>
  • Tidy up of centre of rotation issues and optimisation of iterative code with Diamond NeXuS data sets for integration with DAWN. Q4 2014 and 3.2; Port of Manchester filtered back projection into NeXuS? package as an option with DAWN - Q1 2015) Q4 2014
 
  • Iterative code up and working for the Nikon XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work - can tackle problems with fewer images.
  • Work with Tristan Lowe in Manchester to define a beta version (in the ccpforge) - (Release data release version Q1 2015) Q2 2014
Changed:
<
<
  • 5. Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in !VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3 - Q3 2014
  • Implementation of two/three further quantification algorithms for and from the community (Extra item 7.1 Potential to support Avizo, !ImageJ and !ParaView. Note simpleITK package is supposed to allow ITK functionality to be called from Java so it might be possible to have common packaging of the algorithms) - Q3 2014
  • Capture an idealised dataset - suggested minimum of 2048 images each comprising 8 frames so that we could for example compare reconstructing 2048 1 frame projections with 1024 (each 2 frames summed) projections with 512 (each 4 frames summed) projections with 256 (each 8 frames summed) projections. Possibly with Diamond (Mark Bashham) - Q4 2014
  • Iterative code for the Nikon XTek X-Ray CT Released Q1 2015 - Now that the CPU versions of the reconstruction are under control - accelerated versions (OpenCL, Xeon Phi) should be on the 2015 plan.
  • DAWN integration is on this 2014 plan but should probably be ongoing.
>
>
  • Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in !VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3 - Q3 2014
  • Implementation of two/three further quantification algorithms for and from the community (Extra; potential to support Avizo, !ImageJ and !ParaView) - Q3 2014
  • Capture multiple idealised datasets - initial version has a minimum of 2048 images each comprising 8 frames so that we could for example compare reconstructing 2048 1 frame projections with 1024 (each 2 frames summed) projections with 512 (each 4 frames summed) projections with 256 (each 8 frames summed) projections [with Diamond (Mark Bashham) - Q4 2014] conting Q2 2015
  • Iterative code for the Nikon XTek X-Ray CT Released Q1 2015 - Now that the CPU versions of the reconstruction are under control - accelerated versions (OpenCL, Xeon Phi) should be on the 2015 plan.
  • DAWN integration is on this 2014 plan but will be ongoing.
  • Optimise projection algorithm at the core of iterative routines for an accelerated architecture (GPU/Phi) Q1 2014. The optimised Diamond version has been tested on Xeon Phi and further work tests will occur as part of the ongoing optimisation.
 
Changed:
<
<
CCP_pet/mr Milestone Dates
>
>
CCP_PET/MR Milestone Dates
 
  • Establish website, mailing lists, source code archives
  • Establish database for both simulated and acquired data (i.e. set-up of framework, will slowly be filled over the project)
Line: 92 to 92
 
  • Secretariat Coordination 0.2
  • Basic maintaining network, website, organising administration for workshops and training courses, 0.175
Changed:
<
<
  • Benchmarking, licensing issues 0.525
  • CCPi Framework Developing and maintaining the 3D image analysis toolbox 0.8
  • CCP_petem Developing and maintaining the image reconstruction toolbox 0.8
>
>
  • Benchmarking, profiling, licensing issues 0.525
  • CCPi Framework Developing and maintaining the 3D image analysis toolbox; noise preprocessing, reconstruction and qpost-quantification 0.8
  • CCP_PET/MR Developing and maintaining the image reconstruction toolbox 0.8
  Total 2.5 FTEs
Line: 103 to 103
 
  • Martin Turner 0.2
  • Barry Searle 0.5
  • Srikanth Nagella 0.5
Changed:
<
<
  • Ron Fowler 0.5
  • Ron Hate 0.625
>
>
  • Ron Fowler 0.325
  • Ron Hate 0.8
 
  • Returned to Core SLA activities website etc. 0.175
Changed:
<
<
Total 2.5 fTEs
>
>
Total 2.5 FTEs
  -- MartinTurner - 09 Jan 2015

Revision 312 Jan 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="CCPiTomo"
Changed:
<
<
CCPi.
>
>
CCPi
 
Changed:
<
<
Staffing: The project is proceeding as planned has a strong links with core developers Barry Searle (based at DL), Srikanth Nagella and Ronald Fowler (based at RAL). Over the last year due to an underspend we have had 0.2 FTE Martin Turner and 0.45 FTE Erica Yang.
>
>
Staffing: The project is proceeding as planned and now has a strong links with the core developers; 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 resources for 0.2 FTE Martin Turner for extra secretariate roles and 0.45 FTE Erica Yang for tomographic links with the ISIS (Neutron spallation source) IMAT beamline.
 
Changed:
<
<
Administration: Working group meetings were organised during Q2 and Q4 2014: A series of developers workshop have continues on a quarterly basis: 14th Jan 2014and 20th May 2014 in Birmingham; 22 July 2014 at Nottingham and 22 October 2014 in QMUL. We are also assisting in the second Tomography for Scientific Advancement symposium (ToScA) meeting in the Natural History Museum (1-3 Sep 2014). A monthly showcase involving software show-and-tells were organised at RAL has continued and there are 18 events in the series; including at the end two recorded sessions (47 external views).
>
>
Administration: Working group meetings were organised during Q2 and Q4 of 2014; a series of developers workshop have continues on a quarterly basis: 14 Jan 2014 and 20May 2014 in Birmingham; 22 July 2014 at Nottingham and 22 October 2014 in QMUL; and we also assisted 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 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 (48 external views).
 
Changed:
<
<
Collaboration: contact has continued between CCPi and CCP-ASEArch. A CCPi Seminar was held Nov 2013 and starting in April 2014 was work 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)..
>
>
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).
 
Changed:
<
<
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), with seven under peer review: Theme Issue is titled "X-ray Tomographic Reconstruction for Materials Science".
>
>
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".
 
Changed:
<
<
Development targets met:
>
>
Training etc: A series of courses have been coordinated and software support, including licenses servers, have assisted the Diamond Light Source, Research Compex at Harwell and University of Manchester.
 
Changed:
<
<
  • Initial particle tracking code based on MXIF is complete and in use. Modifications will be made to generalise function to determine proximity of particles from one form to the next.
  • We are implementing histogram based thresholding methods including those from ITK, and further tools are ongoing.
  • Iterative reconstruction development proceeds; we have completed a NeXus? reader for Diamond Light Source data sets; and have run test Diamond data sets on the Hartree Centre ScaleMP? node (order 1TB RAM), where iterative methods require about 20hrs/iteration. The code has been modified to reduce memory requirements for workstations and for the following stage required optimisation to reduce compute cost per iteration which is currently ongoing.
  • The external profile of the project has been raised by updating the CCPi website and creating a dedicated CCPi YouTube? channel:http://www.youtube.com/channel/UCGB578xcyXNQyiBsufEFIeQ
  • Modify CGLS code to analyse example Diamond data set complete by Q3 2013.
>
>
Development targets met for CCPi up to January 2015:

  • 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 is implemented with extended versions planned for 2015.
  • Iterative reconstruction development proceeds; a NeXus? reader for Diamond Light Source data sets is written and deployed; integrated with a CGLS code to analyse Diamond data sets.
  • Test runs on Hartee systems for iterative methods continue and require about about 20hrs/iteration. The code has been modified to reduce memory requirements for workstations and next stage is looking at alternative technologies.
  • A dedicated CCPi YouTube? channel continues to be exploited:http://www.youtube.com/channel/UCGB578xcyXNQyiBsufEFIeQ
 
  • Optimise projection algorithm at the core of iterative routines for an accelerated architecture (GPU/Phi) Q1 2014. The optimised Diamond version has been tested on Xeon Phi and further work tests will occur as part of the ongoing optimisation.
Changed:
<
<
  • Added two new iterative reconstruction algorithms from network members or flagship project to reconstruction suite (Q1 2014). At a developers' meeting in Manchester in March it was discussed how the developer/flagship PDRA should integrate their algorithms into the CCPForge archive and a way forward is being used.
>
>
  • Added two new iterative reconstruction algorithms from network members and flagship project and on the CCPForge.
 

Metrics 2013/4 need values for 2014/5

FOR ALL CCPs. We would highlight that during the financial year 2013/4 (figures from last year’s report in brackets):

Line: 37 to 39
 

Technical Appendix plans for 2015

Changed:
<
<
CCPi – Tomographic Imaging
>
>
CCPi – Tomographic Imaging - and CCP pet/mr
 
Changed:
<
<
Non destructive 3D X-ray imaging is becoming increasingly important in many areas of science and its application to Energy, Healthcare and Security. For example it is 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).
>
>
Non destructive 3D X-ray, Neutron, PET and MR imaging is 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).
 
Changed:
<
<
This CCP aims to provide a toolbox of algorithms that increase the quality and level of information that can be extracted from computer tomography. The CCP will bring together the imaging community, maximise return on investment in software development and ensure longevity, sustainability and re-use of code.
>
>
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.
  Outline of Proposed Core Support Activities:
Changed:
<
<
Most people who acquire and analyse X-ray images have little or no knowledge of X-ray tomography reconstruction and analysis, consequently the involvement of the Core Support is critical if we are to achieve a significant step jump in the level of information obtained by UK science from X-ray imaging. As well as administrative support for the CCP (organization of working group meetings, maintenance of web sites), the core support team (1.5 FTE per annum) at DL will:
>
>
Most people who acquire and analyse images have little or no knowledge of the type of tomography reconstruction or analysis; consequently the involvement of the Core Support is critical if we are 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;
Line: 53 to 55
 
  • 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;
Changed:
<
<
  • Encourage CCP participants to make their algorithms and code available;
  • Create a gallery of test real x-ray image test object datasets for mathematicians to test and benchmark new algorithms; and
>
>
  • 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.
Changed:
<
<
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 0.5FTE for maintaining network, website, running workshops and training course, benchmarking, licensing issues etc; 0.5FTE for developing and maintaining the 3D image analysis toolbox, 0.5FTE for developing and maintaining the image reconstruction toolbox.
>
>
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 0.5FTE for maintaining network, website, running workshops and training course, benchmarking, licensing issues etc; 0.5FTE for developing and maintaining the 3D image analysis toolbox, 0.5FTE for developing and maintaining the image reconstruction toolbox.

For CCP pet/mr: this project ...

  CCPi Milestone Date
Line: 70 to 74
 
  • 5. Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in !VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3 - Q3 2014
  • Implementation of two/three further quantification algorithms for and from the community (Extra item 7.1 Potential to support Avizo, !ImageJ and !ParaView. Note simpleITK package is supposed to allow ITK functionality to be called from Java so it might be possible to have common packaging of the algorithms) - Q3 2014
  • Capture an idealised dataset - suggested minimum of 2048 images each comprising 8 frames so that we could for example compare reconstructing 2048 1 frame projections with 1024 (each 2 frames summed) projections with 512 (each 4 frames summed) projections with 256 (each 8 frames summed) projections. Possibly with Diamond (Mark Bashham) - Q4 2014
Changed:
<
<
  • Iterative code for the Nikon XTek X-Ray CT Released Q1 2015
>
>
  • Iterative code for the Nikon XTek X-Ray CT Released Q1 2015 - Now that the CPU versions of the reconstruction are under control - accelerated versions (OpenCL, Xeon Phi) should be on the 2015 plan.
  • DAWN integration is on this 2014 plan but should probably be ongoing.

CCP_pet/mr Milestone Dates

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

  • Secretariat Coordination 0.2
  • Basic maintaining network, website, organising administration for workshops and training courses, 0.175
Changed:
<
<
  • benchmarking, licencing issues 0.5
  • CCPi Framework Developing and maintaining the 3D image analysis toolbox 0.5
  • CCP_petem Developing and maintaining the image reconstruction toolbox 0.5
  • Evaluation of neutron imaging software 0.25 (Yang)
>
>
  • Benchmarking, licensing issues 0.525
  • CCPi Framework Developing and maintaining the 3D image analysis toolbox 0.8
  • CCP_petem Developing and maintaining the image reconstruction toolbox 0.8
  Total 2.5 FTEs
Line: 92 to 107
 
  • Ron Hate 0.625
  • Returned to Core SLA activities website etc. 0.175
Changed:
<
<
Total 2.5
>
>
Total 2.5 fTEs
  -- MartinTurner - 09 Jan 2015 \ No newline at end of file

Revision 212 Jan 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="CCPiTomo"
Changed:
<
<
CCPi
>
>
CCPi.
  Staffing: The project is proceeding as planned has a strong links with core developers Barry Searle (based at DL), Srikanth Nagella and Ronald Fowler (based at RAL). Over the last year due to an underspend we have had 0.2 FTE Martin Turner and 0.45 FTE Erica Yang.
Line: 37 to 37
 

Technical Appendix plans for 2015

Changed:
<
<
CCPi – Tomographic Imaging
>
>
CCPi – Tomographic Imaging
  Non destructive 3D X-ray imaging is becoming increasingly important in many areas of science and its application to Energy, Healthcare and Security. For example it is 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).

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

Changed:
<
<
Outline of Proposed Core Support Activities:
>
>
Outline of Proposed Core Support Activities:
  Most people who acquire and analyse X-ray images have little or no knowledge of X-ray tomography reconstruction and analysis, consequently the involvement of the Core Support is critical if we are to achieve a significant step jump in the level of information obtained by UK science from X-ray imaging. As well as administrative support for the CCP (organization of working group meetings, maintenance of web sites), the core support team (1.5 FTE per annum) at DL will:
Line: 59 to 59
  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 0.5FTE for maintaining network, website, running workshops and training course, benchmarking, licensing issues etc; 0.5FTE for developing and maintaining the 3D image analysis toolbox, 0.5FTE for developing and maintaining the image reconstruction toolbox.
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CCPi Milestone Date
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CCPi Milestone Date
 
  • 1 Organise working group meeting/ ToScA involvement, and monthly show-and-tell sessions - Ongoing
  • 2. 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) - Q4 2014
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  • Capture an idealised dataset - suggested minimum of 2048 images each comprising 8 frames so that we could for example compare reconstructing 2048 1 frame projections with 1024 (each 2 frames summed) projections with 512 (each 4 frames summed) projections with 256 (each 8 frames summed) projections. Possibly with Diamond (Mark Bashham) - Q4 2014
  • Iterative code for the Nikon XTek X-Ray CT Released Q1 2015
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Task Effort
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Task Effort
 
  • Secretariat Coordination 0.2
  • Basic maintaining network, website, organising administration for workshops and training courses, 0.175
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  Total 2.5 FTEs
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Staffing Effort
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Staffing Effort
 
  • Martin Turner 0.2
  • Barry Searle 0.5

Revision 109 Jan 2015 - MartinTurner

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META TOPICPARENT name="CCPiTomo"
CCPi

Staffing: The project is proceeding as planned has a strong links with core developers Barry Searle (based at DL), Srikanth Nagella and Ronald Fowler (based at RAL). Over the last year due to an underspend we have had 0.2 FTE Martin Turner and 0.45 FTE Erica Yang.

Administration: Working group meetings were organised during Q2 and Q4 2014: A series of developers workshop have continues on a quarterly basis: 14th Jan 2014and 20th May 2014 in Birmingham; 22 July 2014 at Nottingham and 22 October 2014 in QMUL. We are also assisting in the second Tomography for Scientific Advancement symposium (ToScA) meeting in the Natural History Museum (1-3 Sep 2014). A monthly showcase involving software show-and-tells were organised at RAL has continued and there are 18 events in the series; including at the end two recorded sessions (47 external views).

Collaboration: contact has continued between CCPi and CCP-ASEArch. A CCPi Seminar was held Nov 2013 and starting in April 2014 was work 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)..

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), with seven under peer review: Theme Issue is titled "X-ray Tomographic Reconstruction for Materials Science".

Development targets met:

  • Initial particle tracking code based on MXIF is complete and in use. Modifications will be made to generalise function to determine proximity of particles from one form to the next.
  • We are implementing histogram based thresholding methods including those from ITK, and further tools are ongoing.
  • Iterative reconstruction development proceeds; we have completed a NeXus? reader for Diamond Light Source data sets; and have run test Diamond data sets on the Hartree Centre ScaleMP? node (order 1TB RAM), where iterative methods require about 20hrs/iteration. The code has been modified to reduce memory requirements for workstations and for the following stage required optimisation to reduce compute cost per iteration which is currently ongoing.
  • The external profile of the project has been raised by updating the CCPi website and creating a dedicated CCPi YouTube? channel:http://www.youtube.com/channel/UCGB578xcyXNQyiBsufEFIeQ
  • Modify CGLS code to analyse example Diamond data set complete by Q3 2013.
  • Optimise projection algorithm at the core of iterative routines for an accelerated architecture (GPU/Phi) Q1 2014. The optimised Diamond version has been tested on Xeon Phi and further work tests will occur as part of the ongoing optimisation.
  • Added two new iterative reconstruction algorithms from network members or flagship project to reconstruction suite (Q1 2014). At a developers' meeting in Manchester in March it was discussed how the developer/flagship PDRA should integrate their algorithms into the CCPForge archive and a way forward is being used.

Metrics 2013/4 need values for 2014/5

FOR ALL CCPs. We would highlight that during the financial year 2013/4 (figures from last year’s report in brackets):

  • STFC staff have produced some 51 (107) publications not including papers in preparation
  • STFC staff have given some 101 (109) presentations at meetings ranging from informal site visits to invited talks at major conferences.
  • There are some 1629 (1497) publications that reference codes developed through the SLA
  • Some 4451 (3732) training days covering !PhD supervision, code workshops and scientific meetings.

NEED metrics for CCPi.

April 2014- March 2015



Technical Appendix plans for 2015

CCPi – Tomographic Imaging

Non destructive 3D X-ray imaging is becoming increasingly important in many areas of science and its application to Energy, Healthcare and Security. For example it is 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).

This CCP aims to provide a toolbox of algorithms that increase the quality and level of information that can be extracted from computer tomography. The CCP 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 X-ray images have little or no knowledge of X-ray tomography reconstruction and analysis, consequently the involvement of the Core Support is critical if we are to achieve a significant step jump in the level of information obtained by UK science from X-ray imaging. As well as administrative support for the CCP (organization of working group meetings, maintenance of web sites), the core support team (1.5 FTE per annum) at DL 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 CCP participants to make their algorithms and code available;
  • Create a gallery of test real x-ray image test object datasets for mathematicians to test and benchmark new algorithms; and
  • Maintain documentation.

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 0.5FTE for maintaining network, website, running workshops and training course, benchmarking, licensing issues etc; 0.5FTE for developing and maintaining the 3D image analysis toolbox, 0.5FTE for developing and maintaining the image reconstruction toolbox.

CCPi Milestone Date

  • 1 Organise working group meeting/ ToScA involvement, and monthly show-and-tell sessions - Ongoing
  • 2. 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) - Q4 2014
  • Port 3 or 4 iterative codes so that they can be compared on the same datasets
  • Extra targets: 3.1 Tidy up of centre of rotation issues and optimisation of iterative code with Diamond NeXuS data sets for integration with DAWN. Q4 2014 and 3.2; Port of Manchester filtered back projection into NeXuS? package as an option with DAWN - Q1 2015) Q4 2014
  • Iterative code up and working for the Nikon XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work - can tackle problems with fewer images.
  • Work with Tristan Lowe in Manchester to define a beta version (in the ccpforge) - (Release data release version Q1 2015) Q2 2014
  • 5. Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in !VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3 - Q3 2014
  • Implementation of two/three further quantification algorithms for and from the community (Extra item 7.1 Potential to support Avizo, !ImageJ and !ParaView. Note simpleITK package is supposed to allow ITK functionality to be called from Java so it might be possible to have common packaging of the algorithms) - Q3 2014
  • Capture an idealised dataset - suggested minimum of 2048 images each comprising 8 frames so that we could for example compare reconstructing 2048 1 frame projections with 1024 (each 2 frames summed) projections with 512 (each 4 frames summed) projections with 256 (each 8 frames summed) projections. Possibly with Diamond (Mark Bashham) - Q4 2014
  • Iterative code for the Nikon XTek X-Ray CT Released Q1 2015

Task Effort

  • Secretariat Coordination 0.2
  • Basic maintaining network, website, organising administration for workshops and training courses, 0.175
  • benchmarking, licencing issues 0.5
  • CCPi Framework Developing and maintaining the 3D image analysis toolbox 0.5
  • CCP_petem Developing and maintaining the image reconstruction toolbox 0.5
  • Evaluation of neutron imaging software 0.25 (Yang)

Total 2.5 FTEs

Staffing Effort

  • Martin Turner 0.2
  • Barry Searle 0.5
  • Srikanth Nagella 0.5
  • Ron Fowler 0.5
  • Ron Hate 0.625
  • Returned to Core SLA activities website etc. 0.175

Total 2.5

-- MartinTurner - 09 Jan 2015

 
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