Difference: ChairReportJune2015 (1 vs. 8)

Revision 816 Jun 2015 - MartinTurner

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

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

Line: 77 to 77
  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 project and research proposals need to be submitted.
Changed:
<
<
  • Applications for new Fellowships and exchange visits are needed.
  • Software licences are an issue including the Avizo site license that expires at the end of March 2016.
>
>
  • Applications for ‘good’ new Fellowships and exchange visits are difficult and needed.
  • CCP website consistency could be improved across CCPs and further advertisement..
  • Inner-core level SLA support for follow-on phase needs clarification.
  • Software licences are an issue including the Avizo Harwell Campus site license that expires in 2016..
  The next CCPi Working Group meeting is planned to be held in December 2015; with a mini-session planned during the change of phase around August 28 2015.

Revision 716 Jun 2015 - MartinTurner

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

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

Line: 8 to 8
  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.
Changed:
<
<
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.
>
>
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 the 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.
Line: 19 to 19
 
  • 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.
  • 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.
Changed:
<
<
  • 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.
>
>
  • A new data archive with community space has been setup on the zenodo website https://zenodo.org/collection/user-ccpi?ln=en This site includes test data sets from Sophia Coban; simple model scans and touchtable presentation data sets for science analysis and for public outreach and dissemination.
 
Changed:
<
<
The coding work is now producing three different Frameworks for researchers to use, depending on imaging system used:
>
>
The coding work is now producing three different Frameworks for researchers, depending on imaging system used:
 
Changed:
<
<
  1. Diamond framework Savu: progress has speeded up with the recruitment of Nicola Wadeson to assist Mark Basham and immediate future code will address speed including parallel performance as well as ring artefact codes.
>
>
  1. Diamond framework Savu: progress has speeded up with the recruitment of Nicola Wadeson to assist Mark Basham and immediate future code will address speed including parallel performance as well as integrated ring artefact codes.
 
  1. ISIS IMAT framework: Srikanth Nagella built the initial testbed for rendering large data sets (2000^3) and a new setup will be operating in September 2015. The initial IMAT demonstrator has a project page at: http://stfc.ac.uk/SCD/research/data/44593.aspx and new publications are planned.
Changed:
<
<
  1. Avizo framework (at the University of Manchester): the complete framework is being ported within the Avizo visualisation system with interfaces for reconstruction code, segmentation and the beam-hardening sensitivity functions.
>
>
  1. Avizo framework (University of Manchester): a complete framework is being ported within the Avizo visualisation system with interfaces for reconstruction code, segmentation and the beam-hardening sensitivity functions.
 

Outreach and networking:

Line: 39 to 39
 
  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).
Changed:
<
<
  1. Developers' Day at Manchester Workshop focused on iterative solutions for the XTek machines (such as the released CGLS code) and what is required to get them into regular usage in the labs that use these machines (28 April 2015).
>
>
  1. A Manchester Workshop focused on iterative solutions for the XTek machines (such as the released CGLS code) and planned the requirements to get them into regular usage in the labs that use these machines (28 April 2015).
 
  • Fellowships: Manuch Solemani has have some time to edit the Royal Society Phil Trans A special edition that is now published; Brian Bay, from !LaVision Inc., continued his tour in the UK; the scheme will assist the Drishti volume visualiser author Ajay Limaye, visit in September 2015; two members from the University of Bordeaux, Erwan Plougonven (Dec 2014) and Dominique Bernard (February 2015), visited the UK to exchange experiences on source code integration for quantification visualisation; and Nicola Wadeson updated work for source code to make the Rapiscan RTT x-ray CT Machine usable as an experimental system (Feb-May 2015). Also Daniil Kazantsev has agreed to extend his fellowship until the end of August 2015.
  • EU involvement: There has been exchanges with the EU e-COST programme (EXTREME) with collaborating through workshops and conferences (links through Bill Lionheart, Mark Basham and Daniil Kazantsev). Formal meetings have occurred at the Applied Inverse Problems 2015 conference.
Line: 49 to 49
 
  • CCP-ASEArch collaboration: Starting in April 2014 work, by Evgueni Ovtchinnikov, involves numerical methods, to apply a multigrid solution to improve the issues caused by gradient based regularization coefficients in order to accelerate and stabilise convergence is complete with a a publication submitted (collaboration with Daniil Kazantsev - CCPi Flagship Fellow).
  • The SLA EPSRC funded survey: the results for CCP visualisation user needs has been analysed to consider the long tail of products that the global community uses (>100 responses) and focus our CCPi core development effort on certain products. Launched on 2 February 2015: http://www.vizmatters.cs.manchester.ac.uk/index.php/Main_Page
Changed:
<
<
  • Cross-funded links with the HIP (Harwell Imaging Partnership) have provided momentum for the visualisation facilities within the new ICAL (Interdisciplinary Centre for Ancient Life) wit the Manchester Museum.
>
>
  • Cross-funded links with the HIP (Harwell Imaging Partnership) have provided momentum for the visualisation facilities within the new ICAL (Interdisciplinary Centre for Ancient Life) with the Manchester Museum.
 
Industrial Projects:

  • 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).
Changed:
<
<
  • New presentation and links with ...
>
>
  • New discussions have occured with the Avizo developers (FEI) to see about integration of code within their system. Initial meetings occueed and workshop planned for September 2015.
 

Workshops and New Opportunities

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

Changed:
<
<
  • 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
>
>
  • 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.) Partnership status has been applied for and advertisement including leaflets and a stand are being prepared including links with the CCP PET/MR. We will be sponsoring student travel grants.
  • July 8-11, 2015 Harwell Open Days including Tomography vis tools from CCPi and CCP PET/MR will be demonstrated over the days at the Atlas Visualisation Facility
 
  • 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/
Changed:
<
<
  • CLF Vulcan data from recent imaging capture industrial exploitation days. Planned for June/July 2015
>
>
  • Open session for analysis of CLF Vulcan data from recent imaging capture industrial exploitation days is 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:
Changed:
<
<
  • 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.
>
>
  • The 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.
  • 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
Line: 75 to 75
 

Issues and Problems

Changed:
<
<
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.
>
>
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 project and research proposals need to be submitted.
 
Changed:
<
<
  • 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.
>
>
  • Applications for new Fellowships and exchange visits are needed.
  • Software licences are an issue including the Avizo site license that expires at the end of March 2016.
 
Changed:
<
<
The next CCPi Working Group meeting is planned to be held in December 2015; with a mini-session planned over the change of phase around August 28 2015.
>
>
The next CCPi Working Group meeting is planned to be held in December 2015; with a mini-session planned during the change of phase around August 28 2015.
  -- MartinTurner - 03 Jun 2015

Revision 615 Jun 2015 - RonFowler

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

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

Line: 8 to 8
  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.
Changed:
<
<
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.
>
>
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.
Line: 17 to 17
 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.
Changed:
<
<
  • 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.
>
>
  • 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.
Changed:
<
<
  • 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.
>
>
  • 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:
Line: 31 to 31
  Key outcomes:
Changed:
<
<
  • 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
>
>
  • 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.
Changed:
<
<
  • 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).
>
>
  • 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.
Changed:
<
<
  • Developers’ workshop occur each quarter considering a specific focus;
>
>
  • 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).
Line: 53 to 53
 
Industrial Projects:
Changed:
<
<
  • 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).
>
>
  • 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;

Changed:
<
<
  • 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.
>
>
  • 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
Changed:
<
<
  • 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/
>
>
  • 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.
Changed:
<
<
  • A touchtable volume visualisation content discussion mini workshop is planned tpo coincie with the ToScA event .
>
>
  • 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

Changed:
<
<
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.
>
>
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.

Revision 515 Jun 2015 - MartinTurner

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

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

Line: 16 to 16
  Core highlights within the CCPForge software repository:-
Changed:
<
<
  • Reconstruction Core algorithms: The optimisation of the iterative code for Diamond data sets is complete and has been tested on a sequence of reduced projection data from I13. Results have been extended for full sequence as well as creating The Windows GUI for the lab based instruments, with licences created for release to the wider community via a ccpforge download.
  • Quantitative visualisation: 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.
  • 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). A final set of code is being developed to compare algorithms for restricted angle reconstruction.
>
>
  • 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.
  • 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.
  • 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.
 
  • 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.

The coding work is now producing three different Frameworks for researchers to use, depending on imaging system used:

Line: 32 to 32
 Key outcomes:

  • 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
Changed:
<
<
  • 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 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.
>
>
  • 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.
 
  • 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).
  • 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.
  • Developers’ workshop occur each quarter considering a specific focus;
Line: 54 to 54
 
Industrial Projects:

  • 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).
Changed:
<
<
  • New presentation and links with
>
>
  • 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;

Changed:
<
<
* 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.)
>
>
  • 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.
  • 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
  • 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/
  • 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.
  • A touchtable volume visualisation content discussion mini workshop is planned tpo coincie 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
 
Changed:
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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. http://emit.manchester.ac.uk/

* 9 March 2015 for three weeks, CLF Vulcan access for image acquisition

* Continual links with the tomography standards panel (NPL/BSI cttee membership).

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

* Next Away-day developers’ day: Warwick University Manufacturing group to host meeting: also show and tells on frameworks.

* NVidia support through SCD has been offered and will be exploited in a forthcoming the developer’ workshops.

* We are planning on an Avizo and ImageJ API multi-day workshop at Manchester in February involving developers and the software authors/owners to aid code integration;

* A touchtable volume visualisation content creation day in April with four touchtables being commissioned or built across different CCPi partners.

* A ParaView training day and software show-and-tell Kitware Inc (Marcus Hanwell) when author of TomView visits in September 2015

* Funding to build a Rapiscan prototype tomography solution for Nicola Wadeson is agreed to come from the "Computer tomography CCP: widening participation" grant that has a few weeks left, and work is due to start in the next six months.

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

>
>
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

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.

Changed:
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* 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.

>
>
  • 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.
  The next CCPi Working Group meeting is planned to be held in December 2015; with a mini-session planned over the change of phase around August 28 2015.

Revision 415 Jun 2015 - MartinTurner

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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.
Changed:
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The core team now includes Srikanth Nagella, Barry Searle and Ron Fowler with Evgueni Ovtchinnikov stepped forward to assist and work on the follow-on network; creating the core 1.5 FTE. For the year until Spring 2015 Martin Turner has had a role in the secretariat position and with Erica Yang has been developing extra functionality in collaborating with the new IMAT tomographic beamline on the ISIS neutron spallation source. Erca Yang has been given an extension at 0.1 FTE over the following year to continue this role until Spring 2016.
>
>
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.
  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.
Line: 16 to 16
  Core highlights within the CCPForge software repository:-
Changed:
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* OLD Reconstruction Core algorithms: The optimisation of the iterative code for Diamond data sets is complete and has been tested on a sequence of reduced projection data from I13. Results look promising and the full sequence will be processed in 2015 Q1.The Windows GUI for lab based instruments has now been released to the wider community via a ccpforge download. This includes improved projection algorithms based on recent work by Will Thompson at Manchester. As a result a mode of the XTek instrument that is not currently supported has been identified. Support for this mode and other instruments is likely to be discussed at the next developers day.
>
>
  • Reconstruction Core algorithms: The optimisation of the iterative code for Diamond data sets is complete and has been tested on a sequence of reduced projection data from I13. Results have been extended for full sequence as well as creating The Windows GUI for the lab based instruments, with licences created for release to the wider community via a ccpforge download.
  • Quantitative visualisation: 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.
  • 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). A final set of code is being developed to compare algorithms for restricted angle reconstruction.
  • 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.
 
Changed:
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* OLD Quantitative visualisation: work in quantification and the new Avizo algorithms contributed by Erwan Plougonven. study on beam hardening code. Action: RF/SN case study on quantification codes. Action: DK case study for flagship activities.
>
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The coding work is now producing three different Frameworks for researchers to use, depending on imaging system used:
 
Changed:
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Work on supporting the CCPi archive has continued and the current algorithms are available on multiple operating systems (Linux, Windows and Mac) and software products (Avizo, ParaView and ImageJ). Several new algorithms have been identified from the community that would be useful to include in the software repository and discussions held with the developers. A new implementation of a beam hardening correction algorithm (from Graham Davis) is currently being developed, in collaboration with users at RaCH and Leeds University. Another algorithm identified is measurement of tortuosity in 3D tube-like structure from Robert Bradley at MXIF and access to the source code is expected shortly. In collaboration with Diamond, a ParaView reader for NeXus data files has been developed and released.
>
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  1. Diamond framework Savu: progress has speeded up with the recruitment of Nicola Wadeson to assist Mark Basham and immediate future code will address speed including parallel performance as well as ring artefact codes.
  2. ISIS IMAT framework: Srikanth Nagella built the initial testbed for rendering large data sets (2000^3) and a new setup will be operating in September 2015. The initial IMAT demonstrator has a project page at: http://stfc.ac.uk/SCD/research/data/44593.aspx and new publications are planned.
  3. Avizo framework (at the University of Manchester): the complete framework is being ported within the Avizo visualisation system with interfaces for reconstruction code, segmentation and the beam-hardening sensitivity functions.
 
Changed:
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* Flagship project software outcomes: DK reported that 2 papers have been published and 2 more are in progress. Papers include one in Inverse Problems in Imaging and one on CUDA acceleration. PW said it would be good to be able to compare algorithms for restricted angle reconstruction. GD said he knew of a data set from a Nikon machine (for the Antikythera mechanism) with missing projections which can’t be rescanned. It would a useful test case. Action: GD to try and locate data for this* OLD A test tomography reconstruction and remote viewing system for the ISIS neutron spallation source has been complete and a set of evaluation code to create a service is currently being created. The service product is due for operation in April 2015.
>
>

Outreach and networking:

 
Changed:
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* New data archive has been setup: reported that test data sets could now be made available on the zenodo website e.g.https://zenodo.org/record/16539#.VVXi8JPk-RK The above is one of the example data sets Sophia Coban has uploaded to the site.
>
>
Key outcomes:
 
Changed:
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* Attendance at COST Applied Inverse Problems conference at end of May and has organised a session there.
>
>
  • 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
  • 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 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.
  • 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).
  • 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.
  • Developers’ workshop occur each quarter considering a specific focus;
 
Changed:
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The work is now producing three different Frameworks for researchers to use depending on imaging system used:
>
>
  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).
  3. Developers' Day at Manchester Workshop focused on iterative solutions for the XTek machines (such as the released CGLS code) and what is required to get them into regular usage in the labs that use these machines (28 April 2015).
 
Changed:
<
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An initial set of frameworks are being evaluated for inclusion within a future CCPi framework that will constitute a major part of the new CCPi; currently two; the Diamond Light Source savu framework; and the ISIS Neutron IMAT framework are being built for production service roles.
>
>
  • Fellowships: Manuch Solemani has have some time to edit the Royal Society Phil Trans A special edition that is now published; Brian Bay, from !LaVision Inc., continued his tour in the UK; the scheme will assist the Drishti volume visualiser author Ajay Limaye, visit in September 2015; two members from the University of Bordeaux, Erwan Plougonven (Dec 2014) and Dominique Bernard (February 2015), visited the UK to exchange experiences on source code integration for quantification visualisation; and Nicola Wadeson updated work for source code to make the Rapiscan RTT x-ray CT Machine usable as an experimental system (Feb-May 2015). Also Daniil Kazantsev has agreed to extend his fellowship until the end of August 2015.
  • EU involvement: There has been exchanges with the EU e-COST programme (EXTREME) with collaborating through workshops and conferences (links through Bill Lionheart, Mark Basham and Daniil Kazantsev). Formal meetings have occurred at the Applied Inverse Problems 2015 conference.
 
Deleted:
<
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# Diamond framework Savu: progress has speeded up with the recruitment of Nicola Wadeson to assist Mark Basham. MPI performance and other issues will be addressed and ring artefact codes may be added.

# ISIS IMAT framework: SN reported this was progressing well. There were issues with rendering large data sets (2000^3) using just CPU methods so now looking to use GPUs. WK said that IMAT would begin operating in September so the framework needs to be working by then.

The IMAT demonstrator has a project page at: http://stfc.ac.uk/SCD/research/data/44593.aspx

# Avizo framework (UoM): SN reported he was helping with a reader for BS reconstruction code within Avizo. PW noted the importance of segmentation and the sensitivity of simple methods to e.g. beam hardening, changes in machine parameters, etc. Should ask e.g. Avizo for better tools.

Outreach and networking:-

* Phil Trans Journal special issue was released in May specifically on CCPi actuvities based around recontrustion techniques: with a pull-up poster produced. http://rsta.royalsocietypublishing.org/content/373/2043

* CCPi represented at the Cheltenham festival of science and will help at the “Dino zone” there were over six open days; Total public 12,100 and Total with schools 13,755 plus two evening VIP sessions. 1-7 June 2015.

* Workshops / Training; We continue to support training courses from the network from minor software licenses to full training: Mantid Training Courses 16-18 Feb 2015 with a component of tomography vis; Diamond and ISIS have a CDT doctoral training working shop in 9-13 March 2015 with a one 2h introduction and a 2h training session on imaging and visualisation; 16-17 APril Training Diamond Manchester Collaboration, CCPi and HIP, the University of Manchester and Diamond Light Source will be running a 2 day course on the Visualisation and quantification of tomographic data; Tuesday, 9 June 2015 on Avizo training.

* The new series of social meetings at RAL (coffee-and-tomography) has hosted its 23rd monthly meeting (total attendance now at 318). ther ewas also a 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".

* Developers’ workshop occur each quarter considering a specific focus;

# An extended four day Avizo framework developers meeting was held at Manchester hosted by Ali Chirazi. 17-20 February 2015, Developers' Day at Manchester

# Touchscreen day at Reading University was useful and formed a sub-group (IVG – Interactive Visualisation Group) to promote touch screens for outreach, etc. 24 March 2015

# 28 April 2015, Developers' Day at Manchester Workshop that focused on iterative solutions for the XTek machines (such as the released CGLS code) and what is required to get them into regular usage in the labs that use these machines.

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

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

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

 
CCP Cross-collaborations:
Changed:
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* CCP-ASEArch collaboration: Starting in April 2014 this work, by Evgueni Ovtchinnikov, involves numerical methods, to apply a multigrid solution to improve the issues caused by gradient based regularization coefficients in order to accelerate and stabilise convergence. This has now resulted in a publication to be submitted after collaboration with Daniil Kazantsev (CCPi Flagship Fellow).
>
>
  • CCP-ASEArch collaboration: Starting in April 2014 work, by Evgueni Ovtchinnikov, involves numerical methods, to apply a multigrid solution to improve the issues caused by gradient based regularization coefficients in order to accelerate and stabilise convergence is complete with a a publication submitted (collaboration with Daniil Kazantsev - CCPi Flagship Fellow).
  • The SLA EPSRC funded survey: the results for CCP visualisation user needs has been analysed to consider the long tail of products that the global community uses (>100 responses) and focus our CCPi core development effort on certain products. Launched on 2 February 2015: http://www.vizmatters.cs.manchester.ac.uk/index.php/Main_Page
 
Changed:
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* The SLA EPSRC funded survey: the results for CCP visualisation user needs has been analysed to consider the long tail of products that the global community uses (>100 responses) and focus our CCPi core development effort on certain products. Launched on 2 February 2015: http://www.vizmatters.cs.manchester.ac.uk/index.php/Main_Page
Industrial Projects:
>
>
  • Cross-funded links with the HIP (Harwell Imaging Partnership) have provided momentum for the visualisation facilities within the new ICAL (Interdisciplinary Centre for Ancient Life) wit the Manchester Museum.
 
Changed:
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* 30 June 2014 there was a TSB (UK Innovate) Kick-off meeting (project code 37972-241197) for an approved project within the Towards Zero Prototyping programme. Titled 'In silico evaluation of manufacturing concepts for non-Newtonian products' this collaborates with Prof Rob Prosser (University of Manchester), Drs Charles Moulinec and Rob Allan (STFC/SCD), Prof Adam Kowalski (Unilever) and CDDMtec aim to integrate computer CFD simulation, with tomographic 3D image capture; that will add the human-in-the-loop.
>
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Industrial Projects:
 
Changed:
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* New presentation and links with
>
>
  • 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).
  • New presentation and links with
 

Workshops and New Opportunities

Revision 312 Jun 2015 - MartinTurner

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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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Background

Changed:
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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, as well as delivered benefits specified from the mid-term review findings. The CCPi prioritises the two areas of reconstruction and quantitative analysis. It aims to provide the UK tomography community with a toolbox of algorithms that increases the quality and level of information that can be extracted by computer tomography. Key components continue to be to increase usage, training and software deposits, as well as integration of new iterative methods within the toolkits.
>
>
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.
 
Changed:
<
<
The core team for the quantitative analysis as Srikanth Nagella and Ron Fowler have stepped forward and Evgeni xxx creating the core 1.5 FTE. For a year until Spring 2015 Martin Turner has had a role in the secretariat position and with Erica Yang has been developing extra functionality in collaborating with the new IMAT tomographic beamline on the ISIS neutron spallation source. Erca Yang has been given an extension at 0.1 FTE to continue this role.
>
>
The core team now includes Srikanth Nagella, Barry Searle and Ron Fowler with Evgueni Ovtchinnikov stepped forward to assist and work on the follow-on network; creating the core 1.5 FTE. For the year until Spring 2015 Martin Turner has had a role in the secretariat position and with Erica Yang has been developing extra functionality in collaborating with the new IMAT tomographic beamline on the ISIS neutron spallation source. Erca Yang has been given an extension at 0.1 FTE over the following year to continue this role until Spring 2016.
 
Changed:
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There are now formal links with the recently funded CCP PET/MR that employs similar iterative solutions for positron emission tomography (PET) solutions. This has initially involved a joint developers' workshop and now the two CCPs are linking together with shared secretariat roles.
>
>
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.
 

Highlights for the Current Reporting Period

Core highlights within the CCPForge software repository:-

Deleted:
<
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* Attendance at COST Applied Inverse Problems conference at end of May and has organised a session there.
 * OLD Reconstruction Core algorithms: The optimisation of the iterative code for Diamond data sets is complete and has been tested on a sequence of reduced projection data from I13. Results look promising and the full sequence will be processed in 2015 Q1.The Windows GUI for lab based instruments has now been released to the wider community via a ccpforge download. This includes improved projection algorithms based on recent work by Will Thompson at Manchester. As a result a mode of the XTek instrument that is not currently supported has been identified. Support for this mode and other instruments is likely to be discussed at the next developers day.

* OLD Quantitative visualisation: work in quantification and the new Avizo algorithms contributed by Erwan Plougonven. study on beam hardening code. Action: RF/SN case study on quantification codes. Action: DK case study for flagship activities.

Line: 26 to 24
  * Flagship project software outcomes: DK reported that 2 papers have been published and 2 more are in progress. Papers include one in Inverse Problems in Imaging and one on CUDA acceleration. PW said it would be good to be able to compare algorithms for restricted angle reconstruction. GD said he knew of a data set from a Nikon machine (for the Antikythera mechanism) with missing projections which can’t be rescanned. It would a useful test case. Action: GD to try and locate data for this* OLD A test tomography reconstruction and remote viewing system for the ISIS neutron spallation source has been complete and a set of evaluation code to create a service is currently being created. The service product is due for operation in April 2015.
Changed:
<
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* Diamond framework Savu: MB reported that progress had been slower than hoped but now had Nicola Wadeson and a new starter working on the project. MPI performance and other issues will be addressed and ring artefact codes may be added.

ISIS IMAT framework: SN reported this was progressing well. There were issues with rendering large data sets (2000^3) using just CPU methods so now looking to use GPUs. WK said that IMAT would begin operating in September so the framework needs to be working by then.

>
>
* New data archive has been setup: reported that test data sets could now be made available on the zenodo website e.g.https://zenodo.org/record/16539#.VVXi8JPk-RK The above is one of the example data sets Sophia Coban has uploaded to the site.
 
Changed:
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Avizo framework (UoM): SN reported he was helping with a reader for BS reconstruction code within Avizo. PW noted the importance of segmentation and the sensitivity of simple methods to e.g. beam hardening, changes in machine parameters, etc. Should ask e.g. Avizo for better tools.
>
>
* Attendance at COST Applied Inverse Problems conference at end of May and has organised a session there.
 
Changed:
<
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* New data archive has been setup: reported that test data sets could now be made available on the zenodo website e.g. https://zenodo.org/record/16539#.VVXi8JPk-RK The above is one of the example data sets Sophia Coban has uploaded to the site.
>
>
The work is now producing three different Frameworks for researchers to use depending on imaging system used:
  An initial set of frameworks are being evaluated for inclusion within a future CCPi framework that will constitute a major part of the new CCPi; currently two; the Diamond Light Source savu framework; and the ISIS Neutron IMAT framework are being built for production service roles.
Changed:
<
<

Outreach and networking:-

>
>
# Diamond framework Savu: progress has speeded up with the recruitment of Nicola Wadeson to assist Mark Basham. MPI performance and other issues will be addressed and ring artefact codes may be added.
 
Changed:
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*Agenda Item 8 - Phil Trans Journal status MT: The journal issue was released on Thursday. MT hopes to produce a poster of images from the journal. http://rsta.royalsocietypublishing.org/content/373/2043
>
>
# ISIS IMAT framework: SN reported this was progressing well. There were issues with rendering large data sets (2000^3) using just CPU methods so now looking to use GPUs. WK said that IMAT would begin operating in September so the framework needs to be working by then.
 
Changed:
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* CCPi will be represented at the Cheltenham festival of science and will help at the “Dino zone” there
>
>
The IMAT demonstrator has a project page at: http://stfc.ac.uk/SCD/research/data/44593.aspx
 
Changed:
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* The annual Tomography for Scientific Advancement (ToScA) Symposium 1-3 September 2014, hosted at the Natural History Museum, London, UK had CCPi as a sponsor for the student poster competition as well as running a lively exhibition stand.
>
>
# Avizo framework (UoM): SN reported he was helping with a reader for BS reconstruction code within Avizo. PW noted the importance of segmentation and the sensitivity of simple methods to e.g. beam hardening, changes in machine parameters, etc. Should ask e.g. Avizo for better tools.

Outreach and networking:-

 
Changed:
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* Workshops / Training; We continue to support training courses from the network: LC reported that the latest Avizo training session was completely full with 30 attendees. SN reported that Avizo will be giving an update on new developments in Avizo 9 at RAL next week.
>
>
* Phil Trans Journal special issue was released in May specifically on CCPi actuvities based around recontrustion techniques: with a pull-up poster produced. http://rsta.royalsocietypublishing.org/content/373/2043
 
Changed:
<
<
* The new series of social meetings at RAL (coffee-and-tomography) has hosted its 18th monthly meeting (total attendance now at 266). This has included in the last six months the first two recorded seminars, including the Pre-Christmas talk: by Prof Sarah Hainsworth, University of Leicester on "Forensic Applications of micro-computed tomography; Bones, flies and Richard III".
>
>
* CCPi represented at the Cheltenham festival of science and will help at the “Dino zone” there were over six open days; Total public 12,100 and Total with schools 13,755 plus two evening VIP sessions. 1-7 June 2015.

* Workshops / Training; We continue to support training courses from the network from minor software licenses to full training: Mantid Training Courses 16-18 Feb 2015 with a component of tomography vis; Diamond and ISIS have a CDT doctoral training working shop in 9-13 March 2015 with a one 2h introduction and a 2h training session on imaging and visualisation; 16-17 APril Training Diamond Manchester Collaboration, CCPi and HIP, the University of Manchester and Diamond Light Source will be running a 2 day course on the Visualisation and quantification of tomographic data; Tuesday, 9 June 2015 on Avizo training.

* The new series of social meetings at RAL (coffee-and-tomography) has hosted its 23rd monthly meeting (total attendance now at 318). ther ewas also a 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".

  * Developers’ workshop occur each quarter considering a specific focus;
Changed:
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- An extended Avizo framework developers meeting was held at Manchester hosted by Ali Chirazi.
>
>
# An extended four day Avizo framework developers meeting was held at Manchester hosted by Ali Chirazi. 17-20 February 2015, Developers' Day at Manchester
 
Changed:
<
<
- developers days and other activities: Touchscreen day at Reading University was useful and will form sub-group (IVG – Interactive Visualisation Group) to promote touch screens for outreach, etc.
>
>
# Touchscreen day at Reading University was useful and formed a sub-group (IVG – Interactive Visualisation Group) to promote touch screens for outreach, etc. 24 March 2015

# 28 April 2015, Developers' Day at Manchester Workshop that focused on iterative solutions for the XTek machines (such as the released CGLS code) and what is required to get them into regular usage in the labs that use these machines.

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

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

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

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

Total public 12,100

Total with schools 13,755

Industrial Projects:

>
>
* The SLA EPSRC funded survey: the results for CCP visualisation user needs has been analysed to consider the long tail of products that the global community uses (>100 responses) and focus our CCPi core development effort on certain products. Launched on 2 February 2015: http://www.vizmatters.cs.manchester.ac.uk/index.php/Main_Page
Industrial Projects:
  * 30 June 2014 there was a TSB (UK Innovate) Kick-off meeting (project code 37972-241197) for an approved project within the Towards Zero Prototyping programme. Titled 'In silico evaluation of manufacturing concepts for non-Newtonian products' this collaborates with Prof Rob Prosser (University of Manchester), Drs Charles Moulinec and Rob Allan (STFC/SCD), Prof Adam Kowalski (Unilever) and CDDMtec aim to integrate computer CFD simulation, with tomographic 3D image capture; that will add the human-in-the-loop.

* New presentation and links with

Changed:
<
<

Workshops_and_New_Opportunities

>
>

Workshops and New Opportunities

  Future networking and sustainability opportunities include stronger links with industrial and laboratory based resources. This includes;
Line: 90 to 87
  Training and developer's days are to continue as normal but other items also under consideration:
Changed:
<
<
* Next developers’ day: will ask Warwick University Manufacturing group to host meeting: also show and tells on frameworks.
>
>
* Next Away-day developers’ day: Warwick University Manufacturing group to host meeting: also show and tells on frameworks.
  * NVidia support through SCD has been offered and will be exploited in a forthcoming the developer’ workshops.
Line: 104 to 101
  The CCPi has been in negotiations with a new CCP (MR/PET) and both proposals been successful for future funding in the next round of EPSRC networks. We are actively linking joint activities where appropriate for this new venture within the EPSRC SLA grant activities.
Changed:
<
<

Issues_and_Problems

>
>

Issues and Problems

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

Changed:
<
<
The next CCPi working group meeting is to be held in December 2016; with a mini-session planned over the new phase around August 28.
>
>
The next CCPi Working Group meeting is planned to be held in December 2015; with a mini-session planned over the change of phase around August 28 2015.
  -- MartinTurner - 03 Jun 2015

Revision 211 Jun 2015 - MartinTurner

Line: 1 to 1
 
META TOPICPARENT name="CCPiTomo"
---+ Report from CCPi for the Period 8 January 2015 to 24 June 2015
Line: 6 to 6
 

Background

Changed:
<
<
The CCP in Tomographic Imaging is progressing and since the last 6-month report, on 13 May 2014, it has built on current activities to deliver new versions of the core codes, as well as delivered benefits specified from the mid-term review findings. The CCPi prioritises the two areas of reconstruction and quantitative analysis. It aims to provide the UK tomography community with a toolbox of algorithms that increases the quality and level of information that can be extracted by computer tomography. Key components continue to be to increase usage, training and software deposits, as well as integration of new iterative methods within the toolkits.
>
>
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, as well as delivered benefits specified from the mid-term review findings. The CCPi prioritises the two areas of reconstruction and quantitative analysis. It aims to provide the UK tomography community with a toolbox of algorithms that increases the quality and level of information that can be extracted by computer tomography. Key components continue to be to increase usage, training and software deposits, as well as integration of new iterative methods within the toolkits.
 
Changed:
<
<
There has been changes in the core staffing for the quantitative analysis as Srikanth Nagella and Ron Fowler have stepped in to cover this development and porting work creating the core 1.5 FTE. Also since Spring 2014 Martin Turner has had a role in the secretariat position and with Erica Yang has been developing extra functionality in collaborating with the new IMAT tomographic beamline on the ISIS neutron spallation source.
>
>
The core team for the quantitative analysis as Srikanth Nagella and Ron Fowler have stepped forward and Evgeni xxx creating the core 1.5 FTE. For a year until Spring 2015 Martin Turner has had a role in the secretariat position and with Erica Yang has been developing extra functionality in collaborating with the new IMAT tomographic beamline on the ISIS neutron spallation source. Erca Yang has been given an extension at 0.1 FTE to continue this role.
 
Changed:
<
<
There is growing links with the recently funded CCP PET/MR that employs similar iterative solutions for positron emission tomography (PET) solutions. This has initially involved a joint developers' workshop and now the two CCPs are linking together with shared secretariat roles.
>
>
There are now formal links with the recently funded CCP PET/MR that employs similar iterative solutions for positron emission tomography (PET) solutions. This has initially involved a joint developers' workshop and now the two CCPs are linking together with shared secretariat roles.
 
Changed:
<
<

<a name="Highlights_for_the_Current_Repor"></a>Highlights for the Current Reporting Period

>
>

Highlights for the Current Reporting Period

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

* Flagship project software outcomes: DK reported that 2 papers have been published and 2 more are in progress. Papers include one in Inverse Problems in Imaging and one on CUDA acceleration. PW said it would be good to be able to compare algorithms for restricted angle reconstruction. GD said he knew of a data set from a Nikon machine (for the Antikythera mechanism) with missing projections which can’t be rescanned. It would a useful test case. Action: GD to try and locate data for this* OLD A test tomography reconstruction and remote viewing system for the ISIS neutron spallation source has been complete and a set of evaluation code to create a service is currently being created. The service product is due for operation in April 2015.

* Diamond framework Savu: MB reported that progress had been slower than hoped but now had Nicola Wadeson and a new starter working on the project. MPI performance and other issues will be addressed and ring artefact codes may be added.

ISIS IMAT framework: SN reported this was progressing well. There were issues with rendering large data sets (2000^3) using just CPU methods so now looking to use GPUs. WK said that IMAT would begin operating in September so the framework needs to be working by then.

Avizo framework (UoM): SN reported he was helping with a reader for BS reconstruction code within Avizo. PW noted the importance of segmentation and the sensitivity of simple methods to e.g. beam hardening, changes in machine parameters, etc. Should ask e.g. Avizo for better tools.

* New data archive has been setup: reported that test data sets could now be made available on the zenodo website e.g. https://zenodo.org/record/16539#.VVXi8JPk-RK The above is one of the example data sets Sophia Coban has uploaded to the site.

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

Outreach and networking:-

Changed:
<
<
* May 21, 2014 Celebration of The University of Manchester's Queen's Anniversary Prize for "New Techniques in X-ray Imaging of Materials Critical for Power, Transport and other Key Industries".
>
>
*Agenda Item 8 - Phil Trans Journal status MT: The journal issue was released on Thursday. MT hopes to produce a poster of images from the journal. http://rsta.royalsocietypublishing.org/content/373/2043
 
Changed:
<
<
* We manned a stand at the EuroVis (June 2014), hosted by Swansea University in the UK, the 16th annual visualization gathering organized by the Eurographics Working Group on Data Visualization and supported by the IEEE Visualization and Graphics Technical Committee (IEEE VGTC).
>
>
* CCPi will be represented at the Cheltenham festival of science and will help at the “Dino zone” there
  * The annual Tomography for Scientific Advancement (ToScA) Symposium 1-3 September 2014, hosted at the Natural History Museum, London, UK had CCPi as a sponsor for the student poster competition as well as running a lively exhibition stand.
Changed:
<
<
* Workshops / Training; We continue to support training courses from the network: Includes, 1-2 December 2014 As part of the Diamond Manchester Collaboration, CCPi and HIP, the University of Manchester and Diamond Light Source ran a 2 day course on the Visualisation and quantification of tomographic data. The course was based around open-source software (ImageJ) and commercial software Avizo Software
>
>
* Workshops / Training; We continue to support training courses from the network: LC reported that the latest Avizo training session was completely full with 30 attendees. SN reported that Avizo will be giving an update on new developments in Avizo 9 at RAL next week.
  * The new series of social meetings at RAL (coffee-and-tomography) has hosted its 18th monthly meeting (total attendance now at 266). This has included in the last six months the first two recorded seminars, including the Pre-Christmas talk: by Prof Sarah Hainsworth, University of Leicester on "Forensic Applications of micro-computed tomography; Bones, flies and Richard III".
Changed:
<
<
* Developers’ workshop occur each quarter considering a specific focus; 22 October at QMUL related to overlap with PET / SPECT techniques; informal away-day on 22 July 2014 held at Nottingham's Hounsfield Facility; a multi-CT-machine with novel robotic-greenhouse attachment; and on 20 May held at Birmingham considering quantitative algorithms.
>
>
* Developers’ workshop occur each quarter considering a specific focus;

- An extended Avizo framework developers meeting was held at Manchester hosted by Ali Chirazi.

- developers days and other activities: Touchscreen day at Reading University was useful and will form sub-group (IVG – Interactive Visualisation Group) to promote touch screens for outreach, etc.

  Flagship and publication activities: Related to the code integrated within the CCPForge, three papers have been accepted by Daniil Kazantsev including attendance at the Applied Inverse Problems conference, 2015 in Helsinki.; and the Royal Society Phil Trans A special edition now has a complete set of titles and authors (nine), with seven under peer review: Theme Issue is titled "X-ray Tomographic Reconstruction for Materials Science".
Line: 50 to 64
  * CCP-ASEArch collaboration: Starting in April 2014 this work, by Evgueni Ovtchinnikov, involves numerical methods, to apply a multigrid solution to improve the issues caused by gradient based regularization coefficients in order to accelerate and stabilise convergence. This has now resulted in a publication to be submitted after collaboration with Daniil Kazantsev (CCPi Flagship Fellow).
Changed:
<
<
* The SLA EPSRC funded survey: the results for CCP visualisation user needs has been analysed to consider the long tail of products that the global community uses (>100 responses) and focus our CCPi core development effort on certain products.
>
>
* The SLA EPSRC funded survey: the results for CCP visualisation user needs has been analysed to consider the long tail of products that the global community uses (>100 responses) and focus our CCPi core development effort on certain products. Presnated at

Total public 12,100

Total with schools 13,755

  Industrial Projects:

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

Changed:
<
<

<a name="Workshops_and_New_Opportunities"></a>Workshops and New Opportunities

>
>
* 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;
Changed:
<
<
* September 2015 ToScA Symposium number 3 will include further CCPi activities.
>
>
* 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.)
  * 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. http://emit.manchester.ac.uk/
Line: 70 to 90
  Training and developer's days are to continue as normal but other items also under consideration:
Added:
>
>
* Next developers’ day: will ask Warwick University Manufacturing group to host meeting: also show and tells on frameworks.
  * NVidia support through SCD has been offered and will be exploited in a forthcoming the developer’ workshops.

* We are planning on an Avizo and ImageJ API multi-day workshop at Manchester in February involving developers and the software authors/owners to aid code integration;

Line: 82 to 104
  The CCPi has been in negotiations with a new CCP (MR/PET) and both proposals been successful for future funding in the next round of EPSRC networks. We are actively linking joint activities where appropriate for this new venture within the EPSRC SLA grant activities.
Changed:
<
<

<a name="Issues_and_Problems"></a>Issues and Problems

>
>

Issues_and_Problems

  There is a still need to foster inter- and intra-networking between the two groups; the developers group and the user community. This requires improved communication across sites and involvement of remote participants. Increased levels of outreach as well as submitting proposal for increased resources; all are needed to gain a higher level of trust across the partners.
Changed:
<
<
The next CCPi working group meeting is to be held in June 2015; where plans to create better collaboration and agreed focussed outcomes will be decided upon.
>
>
* 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.

The next CCPi working group meeting is to be held in December 2016; with a mini-session planned over the new phase around August 28.

  -- MartinTurner - 03 Jun 2015 \ No newline at end of file

Revision 103 Jun 2015 - MartinTurner

Line: 1 to 1
Added:
>
>
META TOPICPARENT name="CCPiTomo"
---+ Report from CCPi for the Period 8 January 2015 to 24 June 2015

Prof Philip Withers 24 June 2015 http://www.ccpi.ac.uk/

Background

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

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

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

<a name="Highlights_for_the_Current_Repor"></a>Highlights for the Current Reporting Period

Core highlights within the CCPForge software repository:-

* Reconstruction Core algorithms: The optimisation of the iterative code for Diamond data sets is complete and has been tested on a sequence of reduced projection data from I13. Results look promising and the full sequence will be processed in 2015 Q1.The Windows GUI for lab based instruments has now been released to the wider community via a ccpforge download. This includes improved projection algorithms based on recent work by Will Thompson at Manchester. As a result a mode of the XTek instrument that is not currently supported has been identified. Support for this mode and other instruments is likely to be discussed at the next developers day.

* Quantitative visualisation: Work on supporting the CCPi archive has continued and the current algorithms are available on multiple operating systems (Linux, Windows and Mac) and software products (Avizo, ParaView and ImageJ). Several new algorithms have been identified from the community that would be useful to include in the software repository and discussions held with the developers. A new implementation of a beam hardening correction algorithm (from Graham Davis) is currently being developed, in collaboration with users at RaCH and Leeds University. Another algorithm identified is measurement of tortuosity in 3D tube-like structure from Robert Bradley at MXIF and access to the source code is expected shortly. In collaboration with Diamond, a ParaView reader for NeXus data files has been developed and released.

* Flagship project software outcomes: The non-local regularization package (patch-based method) for 2D/3D tomographic reconstruction is available on GPU and CPU. The modified version of the package has been used for improving spatial-temporal resolution of the simulated and real (neutron) data. Two novel methods available for multi-modal reconstruction, which can be useful for image fusion and also hybrid tomographic reconstruction, such as SPECT/CT, PET/MR etc. are being tested. The work continues on embedding the set of regularization tools (CPU and GPU versions) into the CCPi iterative reconstruction code.

* A test tomography reconstruction and remote viewing system for the ISIS neutron spallation source has been complete and a set of evaluation code to create a service is currently being created. The service product is due for operation in April 2015.

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

Outreach and networking:-

* May 21, 2014 Celebration of The University of Manchester's Queen's Anniversary Prize for "New Techniques in X-ray Imaging of Materials Critical for Power, Transport and other Key Industries".

* We manned a stand at the EuroVis (June 2014), hosted by Swansea University in the UK, the 16th annual visualization gathering organized by the Eurographics Working Group on Data Visualization and supported by the IEEE Visualization and Graphics Technical Committee (IEEE VGTC).

* The annual Tomography for Scientific Advancement (ToScA) Symposium 1-3 September 2014, hosted at the Natural History Museum, London, UK had CCPi as a sponsor for the student poster competition as well as running a lively exhibition stand.

* Workshops / Training; We continue to support training courses from the network: Includes, 1-2 December 2014 As part of the Diamond Manchester Collaboration, CCPi and HIP, the University of Manchester and Diamond Light Source ran a 2 day course on the Visualisation and quantification of tomographic data. The course was based around open-source software (ImageJ) and commercial software Avizo Software

* The new series of social meetings at RAL (coffee-and-tomography) has hosted its 18th monthly meeting (total attendance now at 266). This has included in the last six months the first two recorded seminars, including the Pre-Christmas talk: by Prof Sarah Hainsworth, University of Leicester on "Forensic Applications of micro-computed tomography; Bones, flies and Richard III".

* Developers’ workshop occur each quarter considering a specific focus; 22 October at QMUL related to overlap with PET / SPECT techniques; informal away-day on 22 July 2014 held at Nottingham's Hounsfield Facility; a multi-CT-machine with novel robotic-greenhouse attachment; and on 20 May held at Birmingham considering quantitative algorithms.

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

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

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

CCP Cross-collaborations:

* CCP-ASEArch collaboration: Starting in April 2014 this work, by Evgueni Ovtchinnikov, involves numerical methods, to apply a multigrid solution to improve the issues caused by gradient based regularization coefficients in order to accelerate and stabilise convergence. This has now resulted in a publication to be submitted after collaboration with Daniil Kazantsev (CCPi Flagship Fellow).

* The SLA EPSRC funded survey: the results for CCP visualisation user needs has been analysed to consider the long tail of products that the global community uses (>100 responses) and focus our CCPi core development effort on certain products.

Industrial Projects:

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

<a name="Workshops_and_New_Opportunities"></a>Workshops and New Opportunities

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

* September 2015 ToScA Symposium number 3 will include further CCPi activities.

* 30 June - 1 July 2015 EMiT held at University of Manchester: the EMiT (EMerging Technology) conference series brings together experts from all areas of computing to examine how to best take advantage of the changing landscape of computer hardware. http://emit.manchester.ac.uk/

* 9 March 2015 for three weeks, CLF Vulcan access for image acquisition

* Continual links with the tomography standards panel (NPL/BSI cttee membership).

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

* NVidia support through SCD has been offered and will be exploited in a forthcoming the developer’ workshops.

* We are planning on an Avizo and ImageJ API multi-day workshop at Manchester in February involving developers and the software authors/owners to aid code integration;

* A touchtable volume visualisation content creation day in April with four touchtables being commissioned or built across different CCPi partners.

* A ParaView training day and software show-and-tell Kitware Inc (Marcus Hanwell) when author of TomView visits in September 2015

* Funding to build a Rapiscan prototype tomography solution for Nicola Wadeson is agreed to come from the "Computer tomography CCP: widening participation" grant that has a few weeks left, and work is due to start in the next six months.

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

<a name="Issues_and_Problems"></a>Issues and Problems

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

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

-- MartinTurner - 03 Jun 2015

 
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