Difference: ChairReportJune2015 (5 vs. 6)

Revision 615 Jun 2015 - RonFowler

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META TOPICPARENT name="CCPiTomo"

Report from CCPi for the Period 8 January 2015 to 24 June 2015

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  The CCP in Tomographic Imaging is progressing and since the last 6-month report, on 8 January 2015, it has built on current activities to deliver new versions of the core codes; both reconstruction and quantitative analysis. The CCPi prioritises the two areas of reconstruction and quantitative analysis and is currently completing the task list from the original network grant proposal (28 August 2015). It aims to provide the UK tomography community with a toolbox of algorithms that increases the quality and level of information that can be extracted by computer tomography. Key components continue to be to increase components, usage, training and software deposits, as well as integration of new iterative methods within the toolkits.
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The core team now includes Srikanth Nagella, Barry Searle and Ron Fowler with Evgueni Ovtchinnikov stepped forward to assist and also work on the follow-on network; this creates the core 1.5 FTE. For the year until Spring 2015 Martin Turner has had an extra role in the secretariat position and with Erica Yang has been developing functionality in collaborating with the new IMAT tomographic beamline on the ISIS neutron spallation source. Erica Yang has been given an extension at 0.1 FTE over the following year to continue this role until Spring 2016.
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The core team now includes Srikanth Nagella, Barry Searle, Ron Fowler and Evgueni Ovtchinnikov. Evgueni has been brought into the group to assist with CCPi and follow-on networks; this creates the core 1.5 FTE. For the year until Spring 2015 Martin Turner has had an extra role in the secretariat position and, with Erica Yang, has been developing functionality in collaborating with the new IMAT tomographic beamline on the ISIS neutron spallation source. Erica Yang has been given an extension at 0.1 FTE over the following year to continue this role until Spring 2016.
  Formal links are being built with the recently funded CCP PET/MR that employs similar iterative solutions for positron emission tomography (PET) solutions. This has initially involved joint developers' workshops and linking together Working Groups with plans for a shared secretariat role.
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 Core highlights within the CCPForge software repository:-

  • Reconstruction Core algorithms: optimisation work of the iterative code for Diamond data sets is complete and has been tested on a sequence of reduced projection data from I13. Results have been extended for full sequence as well as creating a Windows GUI for the lab based instruments, with licences created for release to the wider community via a ccpforge download.
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  • Quantitative visualisation algorithms: work in quantification and the new Avizo algorithms have been expended with contributuions by Erwan Plougonven, extra code from Robert Bradley (MXIF) and a study on beam hardening code (Queen's Mary). Case studues (EPSRC formal) are being planned and produced on quantification codes, beam hardening amd the flagship activities.
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  • Quantitative visualisation algorithms: work in quantification and the new Avizo algorithms have been expended with contributions by Erwan Plougonven, extra code from Robert Bradley (MXIF) and a study on beam hardening code (Queen Mary). Case studies (EPSRC formal) are being planned and produced on quantification codes, beam hardening and the flagship activities.
 
  • Flagship project software outcomes: Daniil Kazantsev reported that 4 papers have been published or in progress (including one in Inverse Problems in Imaging and one on CUDA acceleration) and a final set of code is being developed to compare algorithms for restricted angle reconstruction.
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  • New data archive with community space has been setup on the zenodo website https://zenodo.org/collection/user-ccpi?ln=en The above includes test data sets Sophia Coban; simple model scans and touchtable presentstion datas sets for science analysis and for public outreach and dissemination.
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  • A new data archive with community space has been setup on the zenodo website https://zenodo.org/collection/user-ccpi?ln=en The above includes test data sets from Sophia Coban; simple model scans and touchtable presentation data sets for science analysis and for public outreach and dissemination.
  The coding work is now producing three different Frameworks for researchers to use, depending on imaging system used:
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  Key outcomes:
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  • Phil Trans Journal special issue with 11 articles was published in May specifically on CCPi activities that were based around recontrustion techniques: with a pull-up poster produced. http://rsta.royalsocietypublishing.org/content/373/2043 Theme issue ‘X-ray tomographic reconstruction for materials science’ compiled and edited by Manuchehr Soleimani
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  • Phil Trans Journal special issue with 11 articles was published in May specifically on CCPi activities that were based around reconstruction techniques: with a pull-up poster produced. http://rsta.royalsocietypublishing.org/content/373/2043 Theme issue ‘X-ray tomographic reconstruction for materials science’ compiled and edited by Manuchehr Soleimani
 
  • CCPi had a prime location at the Cheltenham Festival of Science in the “Dino zone”; Total public attendance was 12,100 and with schools there were 13,755 attending (plus two evening VIP sessions) over 1-7 June 2015. There were ten demonstrators created and presented (four videos and six 3D exploration models), on the CCPi touch-table, with a total of 699 active explorative viewings covering 2,052 mins (34.2 hours) of use.
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  • Workshops / Training; We continue to support training courses within the network, from minor software license amnagement to full training provision: four courses occured during this period - Mantid Training Courses (16-18 February 2015) with a component of tomography vis; Diamond and ISIS CDT doctoral training working shop (9-13 March 2015) with early imaging and visualisation; (16-17 April 2015) Diamond Manchester Collaboration, CCPi and HIP, the University of Manchester and Diamond Light Source training on the visualisation and quantification of tomographic data; and a University of Manchester Avizo training session (9 June 2015).
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  • Workshops / Training; We continue to support training courses within the network, from minor software license management to full training provision: four courses occurred during this period - Mantid Training Courses (16-18 February 2015) with a component of tomography vis; Diamond and ISIS CDT doctoral training working shop (9-13 March 2015) with early imaging and visualisation; (16-17 April 2015) Diamond Manchester Collaboration, CCPi and HIP, the University of Manchester and Diamond Light Source training on the visualisation and quantification of tomographic data; and a University of Manchester Avizo training session (9 June 2015).
 
  • The series of social meetings at RAL (coffee-and-tomography) has now hosted its 23rd monthly meeting (total attendance is at 318). There was also an extra Lunch and Learn seminar, on Friday 27 February, by Dr Martin Turner on “Visualisation Matters - the need to put the human back in the imaging-capture-and-computational loop". The first two video recorded seminars have now been viewed 66 times.
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  • Developers’ workshop occur each quarter considering a specific focus;
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  • Developer workshops occur each quarter considering a specific focus;
 
  1. An extended four day Avizo framework developers meeting was held at Manchester hosted by Ali Chirazi (17-20 February 2015).
  2. Touchscreen day at Reading University with NHM (Natural History Museum) was very useful and formed a sub-group (IVG – Interactive Visualisation Group) to promote touch screens for outreach (24 March 2015).
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Industrial Projects:
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  • The TSB (UK Innovate) project (code 37972-241197) for Towards Zero Prototyping programme. Titled 'In silico evaluation of manufacturing concepts for non-Newtonian products' is a collaborates with Prof Rob Prosser (University of Manchester), Drs Charles Moulinec and Rob Allan (STFC/SCD), Prof Adam Kowalski (Unilever) and CDDMtec aim to integrate computer CFD simulation, with tomographic 3D image capture; that will add the human-in-the-loop with EIT (Empedence Tomography).
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  • The TSB (UK Innovate) project (code 37972-241197) for Towards Zero Prototyping programme. Titled 'In silico evaluation of manufacturing concepts for non-Newtonian products' is a collaborates with Prof Rob Prosser (University of Manchester), Drs Charles Moulinec and Rob Allan (STFC/SCD), Prof Adam Kowalski (Unilever) and CDDMtec aim to integrate computer CFD simulation, with tomographic 3D image capture; that will add the human-in-the-loop with EIT (Electrical Impedance Tomography).
 
  • New presentation and links with ...

Workshops and New Opportunities

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

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  • September 2015 !ToScA Symposium number 3 will include further CCPi activities including two fellowships for software developers' to attend (!ToScA 2015 will be in Manchester and 2016 will be in Bath.) Publicity partnership status has been applied for and advertisement including leaflets and a stand are being prepared invluding links with CCPET/MR. We will be sponsoring student travel grants.
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  • September 2015 !ToScA Symposium number 3 will include further CCPi activities including two fellowships for software developers' to attend (!ToScA 2015 will be in Manchester and 2016 will be in Bath.) Publicity partnership status has been applied for and advertisement including leaflets and a stand are being prepared including links with CCPET/MR. We will be sponsoring student travel grants.
 
  • July 8-11, 2015 Harwell Open Days including Tomography vis tools from CPi and CCP PET/MR will be demonstrated over the days at the Atlas Visualisation Facility
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  • 30 June - 1 July 2015 !EMiT held at University of Manchester: the !EMiT (EMerging Technology) conference series brings together experts from all areas of computing to examine how to best take advantage of the changing landscape of computer hardware that inclueds GU based touchtable interactions that CCPi will be presenting. http://emit.manchester.ac.uk/
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  • 30 June - 1 July 2015 !EMiT held at University of Manchester: the !EMiT (EMerging Technology) conference series brings together experts from all areas of computing to examine how to best take advantage of the changing landscape of computer hardware that includes GUI based touchtable interactions that CCPi will be presenting. http://emit.manchester.ac.uk/
 
  • CLF Vulcan data from recent imaging capture industrial exploitation days. Planned for June/July 2015
  • Continual links with the tomography standards panel (NPL/BSI cttee membership).
  • Training and developer's days are to continue as normal but other items also under consideration:
  • Next Away-day developers’ day is proposed to be at the Warwick University Manufacturing group: and future software show-and-tell events will be based on the three Frameworks.
  • NVidia support through SCD has been offered and will be exploited in a forthcoming the developer’ workshops.
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  • A touchtable volume visualisation content discussion mini workshop is planned tpo coincie with the ToScA event .
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  • A touchtable volume visualisation content discussion mini workshop is planned to coincide with the ToScA event .
 
  • A !ParaView training day and software show-and-tell Kitware Inc (Marcus Hanwell) when author of !TomView visits in September 2015

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

Issues and Problems

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There is a still need to foster inter- and intra-networking between the two groups; the developers group and the user community. We have increased levels of outreach but more proposals need to be submited.
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There is a still need to foster inter- and intra-networking between the two groups; the developers group and the user community. We have increased levels of outreach but more proposals need to be submitted.
 
  • New Fellowships needed: Visiting fellows: LC said that Brian Bay will be visiting later this year. LC may need help with CUDA development from CCPi; will contact SN in September.
  • Avizo site license expires at the end of March 2016; will need to investigate cost and requirements for new license. Action: MT/SN to contact CLF, ISIS, !RCaH, DLS and SCD about interest in and cost of Avizo license.
 
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