CCPi Tomographic Imaging

CCPi links and work carried out by the Visualisation Group within SCD/STFC and related parties. Workplan for core staff for 2014/15 is required and items listed here are from April 2014.

This wiki is a community site to update on administrative (EPSRC / SCD) targets and discussion points.

CCPi 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. There are two parts; reconstruction techniques to create a 3D volume data set from projections and quantification techniques that can extract relevant objective values from these 3D volumes.


CCPi Exec and Working Group meeting December 2016

DRAFT AGENDA Items for Exec Meeting 7 November 2016, 12:30pm – 2pm: agenda then Working Group meeting 21 November 2016, 10am-12:30pm

  • Approval of past six months activities
  • Exchanges
  • Software plan / coding milestones
  • New actions / milestones
  • Web-site
  • Future meetings
  • AOB

Extras:

  • CCPi for software integration
  • Summer school in Tomo at Bath
  • DTI visit - lunch, Prof Soren Schmidt, Prof Markus Strobl, Dr Morten Sales with Prof Bill Lionheart (November 2016)

CCPi Executive Summary, last six months: June 2016-November 2016

Networking and funding activities:

  • There have been eight visitor exchanges as short-term fellows receiving small amounts of travel/subsistence money.
  • One STFC summer student producing an updated Drishti/Prayog manual (zechang.xu) emphasis for ISIS/IMAT –launch 10 Oct – funded by ISIS.
  • Two UoM summer students carried out spiral reconstruction - about three months money requested (Moe, Yngve M.; Lloyd, Ryan) – funded by CCPi.
  • Six seminars (software show-and-tells) events and ToScA organisation (included seven posters and a talk)
  • Five Public Engagement events (including the Manchester Science Festival at end of this month)
  • Link/advertise six training courses, for materials science visualisation.
  • One conference paper published (Eurographics UK) as well as the seven posters (ToScA)

We now have 314 members on the email list after a few reminder emails (some may be dormant).

Website refreshed and data archives in use (zenodo and dropbox for business are now available).

https://www.ccpi.ac.uk/

https://zenodo.org/communities/ccpi/?page=1&size=20

Coding Milestones from the core SLA funds: To be discussed.

Current set for 2016-2017 are:

  1. Website, mailing lists, source code and data archives
  2. Organise working group meeting and monthly joint show-and-tell sessions
  3. Support current training courses and organise developer workshop to teach
  4. Embed framework: ISIS/IMAT
  5. Embed framework: DLS/savu
  6. Embed lab based framework: UoM/ UoS/ UoW
  7. Add quantitative code examples from the community
  8. Add pre-processing stages inc. beamhardening correction experiments at DLS.
  9. Organise the main ToScA conference; September 2016
  10. Optional: Iterative code for the Nikon XTek X-Ray CT accelerated versions (OpenCL, Xeon Phi)
  11. Optional: Optimise OpenCL projection algorithms.

We need to agree on new Milestones (possibly carry forward these) for next year, after 1 April 2017. This has involved about 0.75FTE - with a projected underspend of 0.45FTE – so recruitment is in process. (Note there was a 0.33FTE underspend last year). http://www.jobs.ac.uk/job/AUP545/visualisation-scientist/

Reminder we are asked to collect statistics on training days/presentations by SCD/STFC staff and publications connected to SCD/STFC staff.

Possible Future actions to coordinate

CoI / PI / Working Group support is to be requested to guide in this effort:

  • Project proposal with Drishti (Ajay Limaye) and DLS (Mark Basham) being planned
  • Project linking TIGRE with Bill Lionheart’s spiral reconstruction code
  • Project MIRAN code with CCPi developers (NE-Scientific - Andrea Borsic)
  • Software hacking the Nikon X-ray system (Parmesh Gajjar and Andrew Ramsey)
  • Software linking the original Valeriy Titarenko’s reconstruction code to have a CCPi archive
  • Royal Society special issue: next one
  • New IoP Journal update (~March 2017)
  • ... and links with ToScA sponsors: RMS
  • Workshop: “Quant Across Scales - Link to CCP5 and CCP-EM” (John Purton, Martyn Winn, etc)
  • Rich Tomography proposal (Christopher Egen, Bob Cernic, Daniil Kazantsev etc)
  • ... link to S-J C and MT for sections
  • CECAM event at DL – on Drishti / Avizo? (link to me above)
  • Request to travel to the USA x2 for Berkley workshop: Proposed for Valeriy Titarenko and Sri Nagella (only hotel accommodation)
  • PSI Workshop on Vis etc: submitting an abstract to; https://indico.psi.ch/conferenceCFA.py?confId=4840
  • EU COST grant: application for 2017

Proposals (speculative):

  • Link with Newton Fund (Global Challenge Research Fund) regarding STFC activities
  • Speculative with Innovate UK – Bill Lionheart
  • 3DSIM Inc – additive manufacturing contact (mathematical simulation)
  • Links with CFD groups – links and discussion with groups in UoM and STFC.

List of meetings:

  • EPSRC Software Strategy Workshop, 24 October 2016 in London
  • Working Group Meeting is booked for 21 November 2016: 10am-1pm. A possible speaker(s) is required.
  • SHRI computational needs with Hartree – very speculative idea for cognitive / machine-learning needs from (mike.holmes at KTN); meeting at Imperial, 23 November 2016

Datasets:

  • Use of zenodo CCPi community site (update)
  • QMUL dataset x2

AOB

  • Do we have ideas for a Xmas Speaker?
  • Upload a public space for touchscreen demonstrators
  • MSc project (at UoM)
  • EPSRC case studies as per previous WG minutes
  • New CCPi poster requested
  • Logos on stickers and mugs
  • STFC PE grant for "Fornesic CSI" on tomography... including ISIS users.

Images of News items maintained at: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News

Appendix B – details of events June 2016-November 2016

Three students over the summer

  1. One at RAL – sponsored by ULTRA/IMAT - Resulting in work for the IMAT launch event on 10 October 2016
  2. Two at UoM – sponsored by CCPi - Software development for reconstruction development

Eight CCPi (Short-term) Fellows: most requested small travel funds.

  • 7 October 2016 Seminar. Lucia Mancini beamline scientists of the SYRMEP beamline at the Elettra synchrotron light source
  • 8 September 2016; at RAL AND 12 September 2016 at University of Manchester - Visit by Marcus Hanwell (Kitware Inc) for tomviz.org product show-and-tell
  • "Fringe Meeting": Workshop @RAL on Advances in X-ray Imaging: Expanding the Frontiers of Knowledge 10 June 2016 Thilo Morgenmeyer, Mines ParisTech, France; Simon Jacques, UoM/UK Catalysis Hub; and Nikolay Osipov & Stephane Quilici , Mines ParisTech, France;
  • Round trip for 'hacking Nikon Metrology X-ray Custom bay": Southampton and RAL 8-9 June Parmesh Gajjar , University of Manchester
  • Extra: 8. - Impromptu presentation by visiting lecturer Dr Hamish Carr : May 2016 at RAL. Code for ContourTree manipulation for volumes to create multiple (level set type) isosurfaces.

Seminars: Six seminars badged with CCPi logo

  • Seminar UoM - Lucia Mancini: 7 October (UoM)
  • 12 September (UoM) and 8 September (RAL) 2016 TomVis software demo and discussion by Marcus Hanlam
  • 12 September 2016 Novitom (RAL) on beamline optimisation and 3D capture - host is 3Dmagination
  • 12 August 2016 RAL show-and-tell; TIGRE cone beam CT software in GPU: https://github.com/CERN/TIGRE Ander Biguri and Manuch Soleimani, University of Bath
  • 11 August 2016 RAL CCPi Interactive Vis - Show-and-Tell http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/ProjectsTouchTable
  • Formal seminar: 14 July 2016, DL, Hamish Carr (University of Leeds), "Topological Analysis and Visualisation"

Conference ToScA 5-7 of September 2016, held at the University of Bath. We had two stands and many events during the three days. See Appendix B for images.

Public Engagement; Five events:

  • RCaH's Royal Society exhibit travels to Manchester Science Festival for satellite exhibition on 24-28 October 2016
  • ESOF event at Manchester - CCPi small stand at the Great Hall in the Sackville Street Building
  • Not directly CCPi: July 4-10 2016, Prof Peter Lee’s group from the University of Manchester, together with Diamond Light Source, Liverpool, the Research Complex at Harwell and Unilever are presenting one of the 20 exhibits at the Royal Society’s Summer exhibition, on “4D science”.
  • DL Open Week: 5 July 2016: VIP day; 6-7 July: School days; 9 July Public Day: total of 815 people were given the "vis treatment" over the week.
  • Manchester Brain Box data showing TWO touchscreens with different sets of presentations: https://mcrbrainbox.wordpress.com/ 19 June 2016

Training ; six advertised:

  • FEI Visit and Workshop planned 24 November 2016 - Sri Nagella
  • Avizo courses 13 October 2016 Manchester-Noriko.Griffiths 20 places
  • Pre-ToScA Workshops on Monday 5th September 2016 at the University of Bath Avizo, VGStudio Max and Drishti. Full event with 38 attendees.
  • Avizo courses 16 to 18 August 2016 Manchester: Noriko.Griffiths@manchester.ac.uk 20 places
  • Hartree Summer School - Image Based Modelling examples were shown and described: 28 June 2016: one hour session in afternoon 12 attendees
  • 13 June 2016 Drishti workshop (HMXIF at Manchester, 8 attendees
  • 18 May 2016 HMXF Lunch and Learn and a follow on Training Session with Parmesh Gajjar on hacking the Nikon imaging devices (initially the custom bay units) 7 places .

CCPi Publications:

  • 15-16 September EGUK CGVC - short paper on EPSRC SLA survey results for CCPs presented at Bournemouth.
  • CCPi related posters at ToScA include eight from partners:
    • Willliam Lionheart et al Exact and iterative helical scan reconstruction on the Nikon XTEK
    • Valeriy Titarenko et al Multi-source high speed scans of large objects with Rapiscan RTT 110
    • Mario Sandoval et al 6DoF Input Device Integration for XCT Volume Visualisation
    • Valeriy Titarenko et al Parallelising algorithms for x-ray tomography problems
    • Parmesh Gajjar et al Beyond a black box: 'Hacking' a Nion Metrology X-Ray CT Machine
    • James O'Sullivan et al Visualising the parasitic nematode Trichuris muris using X-ray micro-computed tomography
    • Dan Sykes et al Learning from nature: Time-lapse 3D imaging of the mechanical behaviour of arthropod cuticle
    • Biguri, Ander; Dosanjh, Manjit; Hancock, Steven; Soleimani, Manuchehr: TIGRE: Tomographic Iterative GPU-based Reconstruction toolbox

Extras:

  • Attended the 10 May 2016 Dimensional X-ray Computed Tomography Conference 2016 Venue: National Physical Laboratory Teddington UK.

Email list ( CCPI-MEMBERS@JISCMAIL.AC.UK) has 314 subscribers; 40 new members since June 2016

  1. shanshan.cheng@
  2. luke.rollings@
  3. joseph.monaghan@
  4. thomas.slater-2@
  5. g.poolo@
  6. tobias.starborg@
  7. jason.wild@
  8. A.Raviraj@
  9. Shashidhara.marathe@
  10. matthew.curd@
  11. ryanlloyd294@
  12. martyn.winn@
  13. chenwillcon@
  14. lucia.mancini@
  15. B.Winiarski@
  16. sarah-jane.clelland@
  17. thomas.sorensen@
  18. dan.sykes@
  19. yngve.m.moe@
  20. sara.nonni@
  21. steve.collins@
  22. paul.evans@
  23. ying.wang-4@
  24. thilo.morgeneyer@
  25. fabien.leonard@
  26. vitaliy.mykhaylyk@
  27. razvan.sencu@
  28. parmesh.gajjar@
  29. Noriko.Griffiths@
  30. genoveva.burca@
  31. Neil.Bourne@
  32. joe.kelleher@
  33. alun.ashton@
  34. evgueni.ovtchinnikov@
  35. jenny.woods@
  36. armin.wagner@
  37. alex.cl.leung@
  38. frank.von-delft@
  39. kamel.madi@
  40. wen.zhang-10@

-- MartinTurner - 09 Nov 2016

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