CCPi Tomographic Imaging

CCPi links and work carried out within SCD/STFC and related parties. 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 parts; not least reconstruction techniques to create a 3D volume data set from projections and quantification techniques that can extract relevant objective values from these 3D volumes.

WP_20170612_013cw.jpg

CCPi Exec Meering (October 2018) and Working Group Meeting (19 November 2018 http://www.ccpi.ac.uk/)

Aim of the meetings: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks; proposal for EPSRC case-studies/mid-term report and new bids.

Network targets: # of people / projects to gain impact items - What kind of code and bids: we should be preparing, in terms of best impacts

Working Group Meeting Agenda (19 November 2018)

DRAFT Agenda; 19 November 2018

Meet from 10:30 and setup AV with coffee/biscuits provide at RAL and Manchester locations.

  • 11:00 Minutes and Actions
  • 11:20 Software Launch (release version 1.x)
    • Overview of CIL and Flagship events
    • Request for wish-list items for futture versions
  • 11:35 Invited speaker on (10 mins each)...
    • TBA
  • 12:15 Review of Summer Associated Conferences: new cttee member requests
    • Process Tomography / ToScA? (inc International - USA and Asia) / dXCT / RCaH? "Advances" workshop EGUK September for 2019 and 2020
    • Joint PETMR activities and PETMR joint course at MIC in November 2019 at Manchester
    • ...
  • 12:30 Update on International Review of CoSeC
    • Future grant networks and ... case studies (of networking)
  • 12:40 New networks and proposals
    • Small funds for ToScA? USA
    • ...
    • BILAT USA 4.0 Workshop on US Funding Opportunities for European Researchers - future USA collab
  • 12:50 New Working Group members.
  • 13:00 Access to IMAT and i12, i13, B24
  • 13:10 Administration
    • jiscmail lists and website content etc
    • HPC: SCARF18, Archer access: "constructive critical champion" role.
  • AOB
  • Location for next WG at RAL with Fringe meeting in June 2019
  • ...

COMBINED Lunch available

Please email to attend at Manchester or RAL and confirm catering.

  • 2pm-4pm Flagship round table meeting
  • Speakers on Colour Bay X-Ray CT
  • ...
  • New Bio-Imaging network (announcement at WG)
  • Visit to Imperial - Turing visualisation centre (1 June 2018)
  • ...

Resources:

  • Use Software Outlook - GPU porting / library analysis
  • CCPi benchmarketing on C01 TODO
  • SCARF18 - should be open for SCD runs parallel in principle.

As a participant; your opinion matters so you can have a few mins to raise a concern or issue for discussion - and welcome to send a topic in advance by email; or a spontaneous comment on the day.

Exec Meeting Agenda 2 October 2019, 1pm "To discuss Summer events and coding from the Core and Flagship environment"

Agenda:

1. Network Activities

2. CIL-Core development: linking with Flagship software + papers etc

Including DVC code being ported into CIL

3. New Recruits

Including Machine Learning summer students

4. CCPPETMR/CCPi interaction: PETMR hackathon, code “blend”, new algorithm

5. Contacts with Thomas Blumensath from Southampton for contributing his parallel reconstruction alg

6. B24 and Process Tomography integration (and future synergistic / rich tomography)

7. AOB notices

  • WMG strategic equipment: been awarded and details at Governance Group meeing Jan 2019 (MT/CCPi has been invited)
  • 2 x summer students in ML - presentation for December (lunch-and-learn planned)
  • SAXS funding - Bill Lionhear (accept to visit Cambridge / Oxford and RAL to star project proposal - BL/MT to coordainate)
  • B24 funding / staff request (data through Mark Basham to be coordainate - DK/EP)
  • Parmesh request to visit Swansea and USA !ToScA (Agreed to travel and represeat CCPi)
  • 22 June 2018 Meeting at Huddersfield University and planning for dXCT 2019 and 2020 (Royce to have a stand at 2019 event)
  • Colour Bay meetings (started by BC and Flaghip to be represented)

Also an introduction to work on beamline B24; senior support scientist, Matt Spink, to see if links similar to IMAT can be made. ( Data sete to be made available through EP/MS)

Actions:

  • MT to attend WMG equipment governance group (January 2019)
  • Summer students to present at lunch and learn - 11 December 2018 [along with Nghia Vo]
  • Bill Lionheart to investigate SAXS project - approve travel
  • B24 datset to be investigated (limited angle 150 deg; 500eV to move to 2.5keV) (link DK,EP)
  • Parmesh Gajjar to attend ToScA USA
  • Thomas Blumensath code to be investigated for CIL inclusion (EP to contact then TL/PG)
  • DVC to be integrated, and BSS Fellowship to be aplied for (Deadline 16 October 2018) BB/EP/MT/DK
  • Process Tomography - further integartion by invitation to Bergen group ("low count and high speed is the commonality") BL/MS
  • New proposal "Rich-and-non-linear tomography operators" (BL et al)


Minutes:

1. Network Activities

  • CCPi Fellowships approved and visits: Brian Bay x2 as well as summer visitors (mainly at dXCT).
  • Grants submitted with Letters of Support from CCPi: WMG is approved.
  • Joint CCP hackathon - workshops/events on code integration
  • Lunch-and-Learn and Show-and-Tell events: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/VisSeminars

CCPi conferences and workshops: Summer 2018

  • Advanced Xray Imaging Workshop June 15 2018
  • Fringe meeting June 14 2018: short informal presentations focusing on sharing reconstruction/analytics algorithms across the modalities of use; and consider how improved sharing/lessons/bast-practice can occur
  • dimension XCT conference at Nottingham: July 2018
  • !ToScA symposium: September 2018.
  • EGUK: Computer Graphics & Visual Computing (CGVC) 2018 with XCT keynote: Prof Richard Johnston (Professor in materials science and engineering)
  • 2-6 September 2018 9th World Congress on Industrial Process Tomography at the University of Bath
  • Virtual Quantification (Llion Evans, Swansea) 22 May 2018 First Stakeholder Meeting; 3-4 (training) and 5-6 (users' workshop) September 2018 IBFEM-4i 2018, Swansea http://ibfem.co.uk/2018/
  • 3-4 September 2018 3rd Conference on Research Software Engineering http://rse.ac.uk/conf2018/ with presence at the SCD stand (plus 5 September 2018 Tier-2/Regional HPC Workshop)

2. CIL-Core development: linking with Flagship software

Software: including DVC code being ported into CIL

Extras for Flagship specific development:

Papers etc:

  • !TomoPhantom software and paper: https://github.com/dkazanc/TomoPhantom
  • Multichannel Inverse Imaging paper: http://iopscience.iop.org/article/10.1088/1361-6420/aaba86
  • Parmesh paper: https://aip.scitation.org/doi/full/10.1063/1.5044393
  • Poster at The Software Sustainability Institute Workshop: Impact of international research software collaboration on Tuesday 24th April at the Museum of Science and Industry
  • CCPi posters werer at d-XCT. ToScA and Advances in Xray Imaging Workshop

3. New Recruits

  • Flagship posts x2 been offered (possible start dates 1 Nov 2018 and 1 Dec 2018)
  • Core CCPi role x1.5: New Recruit (apps by 21 October 2018; so potentially start in Jan 2019); Tomas Kulhanek (based at DL) to join (mid Oct - end Dec 2018) and work on continuous integration and also test-cases at Manchester (contact Parmesh Gajjar and Tristan Lowe)

4. AOB

Points Raised with more details: from November 2017 meeting:

Training / Seminar:

  • Workshop ‘Fibre Reinforced Composites: X-ray Imaging and Advanced Fibre Tracking’ that will take place at the Henry Moseley X-ray Imaging Facility on Tuesday 15th May 2018 (34 att)
  • 17 May 2018, 10am-12noon Avizo hands-on session with FEI at RAL
  • 4 July 2018 Seminar at RAL on Digital Volume Correlation by Prof. Brian Bay (Oregon State University)
  • 6 July 2018, 9:30am pre-coffee talk - Remote Visualisation and Analysis of Tomographic Data - Providing Near Data Analysis Environments and Visualisation for Diamond Data; Richard Smith
  • Regular Manchester Avizo courses; 6-7 March 2018; 5-6 June 2018

Other items:

  • EPSRC XCT Tomography Equipment Roadmap https://www.epsrc.ac.uk/newsevents/news/capitalroadmapforx-raycomputedtomography-epsrcusersurvey/
  • ISO / TC 213 WG10 standards meeting at Poland / BSI

Roll-over Future Ideas/Invitations:

  • Flagship workshop: Matthias (Cambridge) and Simon Arridge or Marta Betcke (both UCL). Also invite someone from CWI.
  • Invite ASTRA to UK : "CWI it would be most useful to have the main ASTRA developer Willem Jan Palenstijn"
  • ... or/and Joost Batenburg (COST plans)
  • PETMR - Matthias Erhhardt from Cambridge. Make interested in multichannel tomography.
  • ... also PETMR Flagship developer (Kinetic PETMR reconstruction)
  • UK-US channel, we could consider inviting Emil Sidky from Chicago
  • Sophia to come and give a talk on her work at CWI
  • Bath presentation (joint NPL project)
  • Future Joint Code Sprint at RAL for CIL-Flagship single and multichannel framework reconstruction.
  • New BSS Fellowship aplication with BB

Case Studies:

  • PE activities
  • beam hardening
  • quantifucationn - porosity
  • parts of CIL
  • ULTRA integration

Summer 2018 International-interim revirew items

Resources:

  • Use Software Outlook - GPU porting / library analysis
  • CCPi benchmarketing on C01 TODO
  • SCARF18 - should be open for SCD runs parallel in principle.

Mid term questions - draft answers:

  1. How long has your CCP / HEC existed? Funded since round before this one.
  2. What is the size of your community? I know this is difficult but the Steering Committee re-iterated the importance of having an estimate – however rough. Active user list has increased from 260 to 380 in the last five years. Events listed of network activity on tyne website: http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News
  3. Are you involved in any international collaborations (please provide details)? Partner to an EU COST grant called Extrema; successful and now resubmitted a second proposal April this year; as first COST grant has recently expired.
  4. Are you involved in any eCSE projects (please provide details)? No
  5. Are you involved in any industrial projects (please provide details)? Yes with Rapiscan Inc (Bill Lionheart details) And connections with exhibitor lists for including ten suppliers notable with:- Nikon (Metrology) - code to recode their XCT scanner (used in UoM / Uos and planed for UoHuddersfied)
  6. How many public sector research establishements (PSREs) do you work with (please provide details)? Links with image based modelling through Culham, notable supporting and linking a five year industrial fellowship with Liion Evans (EPSRC), at Swansea University.
  7. Do you undertake any work with the large experimental facilities (please provide details)? Links with DLS and ISIS (IMAT) -both with industrial components. Notabe DLS "Savu" dataflow project and ISIS IMAT / mantid data visualisation project. Core for the new IMAT beamline. Been awarded beamtime at the ISIS IMAT recent call (August 2018) - to be taken in February 2019. Tesing and proving code on new phantom designs.
  8. Do you have any interaction with the RSEs/Software Sustainability Institute (please provide details)? Awarded UK-USA collaboration grant through EPSRC / SSI September 2017. Continual links to kitware inc since based on their Tomviz software product - code to potentially be shared etc.
  9. Do any grants contribute to the development of your codes (please provide details)? Flagship grant is key for experimental work
  10. How many grants have been developed as a result of your work (please provide details)? Might need input from your Chair. To be collated (Bill Lionheart can you do this)
  11. How many CCP/HEC flagship (including their more recent reincarnations) proposals has your CCP/HEC been involved with (please provide details)? Flagship grant has been awarded (twice). List of papers and code available from Daniil Kazantsev.
  12. How many CCP Network Calls have you been part of (please provide details)? Main cross link is CCP PETMR which shares components both software, networking and website.
  13. Are you (or is the software you develop) involved any Hartree Centre projects (please provide details)? Use of software in visualisation facility for three years during Phase 1. Advise for visualisation facility with David Hughes for Phase 2.
  14. Does your CCP/HEC arrange any visits of international researchers (please provide details)? Yes a series of invites. Brian Bay (Ontario) was most recent visitor. Integration of volume correlation code is underway.
  15. Are your codes available to use on ARCHER and/or Tier-2 systems (please provide details)? No - but contacts being made for possible Tier 2 use.

Interview points:

  • Examples of SLA impact specifically
  • Any details of further funding leveraged off the SLA support

Options for future (from Steering Panel; June 2018)

- have a workshop on machine learning/AI of images. I spoke with Daniela Hensen (BBSRC), anne mcgavigan (MRC) there and suggested I will start to work with Mark Girolami (turing) to hold a small focus group in next 3 months or so on this and then maybe hold a larger workshop with bio and medical thereafter.

- Maybe we should also contact Martin Winn at CCPEM too.

- Use CoSeC as the phrase to represent the central support going forwards.

- Lester from Bristol demonstrated jupyter notebooks for connecting and running bits of software (in his case BioSimspace? ) across multiple languages. All calculations done on remote sever accessed by phone, laptop etc via a browser.

Other points:

  • Items for UK-USA exchange https://docs.google.com/document/d/1B-rCyreeLgJ2qN4k6e2BLM20PKtygS3JuLeIOOZuG1I/edit#
  • Rootrack - status.
  • sw route:-> Software x paper: zenodo plus ccpi seminar(s)

Appendix A: List from - May 2018

Email list (CCPI-MEMBERS@JISCMAIL.AC.UK) has 406 subscribers; 46 new members since May 2018

  1. neil.o'brien@
  2. K.Alsop@
  3. alexander.kao@
  4. c.rossides@
  5. v.fernandez@
  6. swhitbread@
  7. 445305@
  8. oliver.larkin@
  9. ch230@
  10. paul.gunning@
  11. dlatron1@
  12. ilias.kounatidis@
  13. fabio.vittoria.12@
  14. saldridge@
  15. 973879@
  16. christopher.thornton@
  17. k.r.hallam@
  18. jflynn@
  19. strgx@
  20. Brian.Bay@
  21. kalpani.vitharana@
  22. chris.morris@
  23. tomas.kulhanek@
  24. ian.belding@
  25. tohru.araki@
  26. ewelina.kosior@
  27. malte.storm@
  28. sultan.mahmood@
  29. seamus.murphy@
  30. dan.symes@
  31. robert.weatherup@
  32. antoine.cornet@
  33. john.flynn@
  34. j.mathew@
  35. ander.biguri@
  36. i.s.charlwood@
  37. r.johnston@
  38. ben.morgan@
  39. naeem.desai@
  40. tom.etheridge@
  41. Ira.Dekker@
  42. Christopher.Price@
  43. Ian.Nicholson@
  44. Elizabeth.Surrey@
  45. rob.akers@
  46. daniel.pooley@

CCPi Working Group meeting 15 May 2018 (11am - http://www.ccpi.ac.uk/node/399)

Flagship meeting after the main WG http://www.ccpi.ac.uk/Flagship

Aim of the meetings: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks; proposal for EPSRC case-studies/mid-term report and new bids.

Network targets: # of people / projects to gain impact items - What kind of code and bids: we should be preparing, in terms of best impacts


Agenda; 15 May 2018, from 11am

Meet from 10:30 and setup AV.

  • 11:00-11:20 Minutes and Actions: period (Nov 2017 - Mar 2018) See last Exec Meeting as combined action list.
  • 11:20-11:35 Software Launch (release version 1.0)
    • Overview of CIL and Flagship events
    • Request for wish-list items for v1.1
  • 11:35:12:15 Invited speaker on (10 mins each)...
    • Chris Race on ML and AI in Materials Science
    • Jakob Jorgensen and Parmesh Gajjar - Laminography reconstruction
    • Alan Kyffin regarding Anvil/repository
    • Brain Bay / Catherine Disney
  • 12:15:12:30 Associated Conferences:
    • EGUK September 2019 - Visual Analytics course with CECAM, at Daresbury Labs
    • Join course with PETMR at MIC in November 2019 at Manchester
    • dXCT - planning for 2019 (Huddersfield?) and 2020 (Manchester?)
    • ToScA 2018 and USA in 2019
  • 12:30-12:40 Update on International Review of CoSeC
    • SLA only: 12 June 2018 draft - 12 July 2018 SLA steering cttee meeting 20 July 2018 updated draft
    • Likely submission on 20 August 2018 with Review on 15 October 2018
    • May require posters, interviews and
    • ... case studies (of networking)
  • 12:40 New networks and proposals
    • Small funds for Llion Evans (lunch),22 May 2018 "Virtual Qualification: First Stakeholder Meeting"
    • Small funds to support for project connected to more efficient ray-tracing techniques. Bill Lionheart
    • BILAT USA 4.0 Workshop on US Funding Opportunities for European Researchers - future USA collab
  • 12:50 New Working Group members - NPL / Neil Bourne / ...
  • 13:00 Access to IMAT and i13
  • 13:10 Administration
    • distibution jiscmail lists
    • website content etc
    • HPC: SCARF18, Archer access.
  • Link to PETMR - SIRF, bug fixes and expanded functionality https://github.com/CCPPETMR/SIRF/blob/master/CHANGES.md
  • AOB
    • Location for next WG at RAL
    • GDPR issues
    • ...

Please email to attend at Manchester or RAL and confirm catering.

  • 2pm-4pm Flagship round table meeting

Additions or for Fringe meeting:

  • Alan Kyffin at SESC Jenkins (Anvil IM) build system (WG)
  • Bath project (Manuch - emailed)
  • New Bio-Imaging network (announcement at WG)
  • Virtual Qualification: First Stakeholder Meeting - 22 May 2018 (announcement at WG)
  • Visit to Huddersfield (22 June 2018)
  • Visit to Imperial - Turing visualisation centre (1 June 2018)
  • ...

Fringe Special announcements (14 June 2018):

  • Maxime Moreaud (French Institute of Petroleum), open source imaging code Plug im! algorithm for filtering, segmentation and quantification, library for generating random multiscale microstructures, easy to batch.

Fringe meeting: short informal presentations focusing on sharing reconstruction/analytics algorithms across the modalities of use; and consider how improved sharing/lessons/bast-practice can occur. Topics like kinetic movement and statistical change, during capture, are of interest across domains but not properly shared.

As a participant; your opinion matters so you can have a few mins to raise a concern or issue for discussion - and welcome to send a topic in advance by email; or a spontaneous comment on the day.

CCPi Exec 29 March 2018 (9:30am - http://www.ccpi.ac.uk/node/405)

Exec Meeting Agenda (Nov 2017 - Mar 2018) 29 March 2018, 9:30am "To discuss the new coding and outcomes from the Core and Flagship environment"

1. Network Activities

  • CCPi Fellowships approved and visits: Hamish Carr (student working on segmentation code; Leeds), Joan Duran (links with Flagship - CCPi travel funded), Jim Nagy?, Marcus Hanwel (tomviz software use), ...
  • Grants submitted with Letters of Support from CCPi: BL proposal, PL network, WMG equipment purchase - Congratulations to Llion Evans for successful fellowship and Marcus Hanwell (UK-USA collaboration) EPSRC travel grant.
  • Joint CCP PETMR workshops on code integration:- 23/3/2018 and follow up at 19 and 20/4/2018

Three CCPi conferences for Summer 2018 now fully planned:

- Advanced Xray Imaging Workshop June 15 2018: speakers; ACTION Requested funds for travel for speakers (same as 2017) FRINGE meeting being planned for June 14, 2018

  • ‘Revealing defect dynamics in laser additive manufacturing by in situ and operando X-ray imaging’, Alex Leung, University of Manchester
  • ‘Digital Volume Correlation: Progress and Challenges’, Francois Hild, University Paris-Saclay
  • ‘Title TBA’ (topic likely to be around image based modelling and integrating automation into workflow), Llion Evans, Swansea University
  • ‘Title TBA’ (topic likely to be tomography of porous systems), Maxime Moreau, French Institute of Petroleum
  • ‘4D tomography applied to magnetic systems’, Kate Dobson, University of Durham
  • ‘Title TBA’ (topic likely to be X-ray imaging of teeth), Shaz Khan, GSK
  • ‘Title TBA’ (topic likely to be around activities at I14 and electron microscopy), Paul Quinn, Diamond Light Source Imaging Group Leader

- Fringe meeting: short informal presentations focusing on sharing reconstruction/analytics algorithms across the modalities of use; and consider how improved sharing/lessons/bast-practice can occur. Topics like kinetic movement and statistical change, during capture, are of interest across CCPs. https://www.eventbrite.co.uk/e/ct-fringe-meeting-tickets-45130551695 Lunch costs requested

- dimension XCT: speakers so far (plus one) July 2018 ACTION Requested funds for travel for students on usual basis

  • Professor Michael McCarthy (Engineering Metrology Solutions) "Performance verification of industrial CT systems"
  • Paul Gunning (Smith & Nephew) "Use of -XCT in the medical devices industry"

- ToScA: speakers etc to be confirmed: September 2018. ACTION Requested funds for meeting 1.5k

Extra CCPi supported meetings:

- EGUK: Computer Graphics & Visual Computing (CGVC) 2018 with XCT keynote: Prof Richard Johnston (Professor in materials science and engineering at Swansea University in the UK. Co-Director of the 10M Advanced Imaging of Materials (AIM) facility at Swansea, of the 13.7M Materials and Manufacturing Academy for postgraduate training, and the STFC Regional Beamline-Bridging Facility. Founder and Director of the Research as Art awards, which have reached over 50 million people worldwide since 2009, A Software Sustainability Institute Fellow, and a previous British Science Association Media Fellow at Nature) "Title: Visualisation in Microscopy – making sense of the invisible world in 3D"

- 2-6 September 2018 9th World Congress on Industrial Process Tomography at the University of Bath

2. CIL-Core development: linking with Flagship software

Software:

  • CIL code restructuring, released with version 0.9.2
  • CIL Reconstruction Framework as discussed on 18/12/17.
    • i. Planning of framework done in January 2018
    • ii. Coding sprint (with Flagship) in March 2018
    • iii. The code is about to be released open source and contains a framework to quickly develop novel reconstruction algorithms. Readers for Xtek and NeXus.
    • iv. Working at Sophiabeads dataset as benchmark
  • A weekly t-con with core team and flagship team is ongoing on Tuesdays 10:30am (open to anyone - started 18 December 2017)

Segmentation:

  • Simpleflex: Working with Prof. Hamish Carr and student to add functionality and quantification tools on the segmented isosurfaces
  • !SurVos: maintain a this segmenting tool developed by Diamond and Nottingham. Created a windows binary for the use of Diamond i14. Currently we maintain this tool because Diamond doesn’t have resources. Do we?

User engagement:

  • Simpleflex segmentation: we have 3 main contacts: Dr. Robert Atwood (diamond i12, I believe), Dr. Nolwenn !LeGall (Manchester working @ Diamond), Prof. Jawei Mi (Hull). Edo is working together with the scientists to guide them using the algorithm. When needed/possible, new functionality is added. The obvious endpoint is to work with the SAVU team to distribute the Simpleflex segmentation within their framework, as both Diamond and Hull have it.
  • Nick Brierly from MTC who expressed interest in CCPi code, has bought a commercial product.

Networking:

  • Strengthened bonds between CCPi and CCPPETMR by sharing code/solutions. CCPi has adhered to the CCPPETMR naming and coding convention in the development of the Reconstruction Framework, so that it could be easily taken by the CCPPETMR. There is an active discussion between the CCP’s about the definition of the objective function for the optimization problem, for which CCPi core and flagship teams have found one solution.

Extras for Flagship specific development:

CCPi Flagship software update presentation: Multi (and single) channel modular optimisation framework Jakob Sauer Jrgensen et al. cil_opti_ccpi_exec.pdf

Inside Regularization Toolbox:

  • C/CUDA open-source modules to perform 2D/3D filtering/regularization.
  • Currently available methods include Rudin-Osher-Fatemi TV and Fast Gradient Projection TV

TomoPhantom software and paper:

Multichannel Inverse Imaging paper: http://iopscience.iop.org/article/10.1088/1361-6420/aaba86

Extra:

  • Liverpool issue with DLS data (request from Robert Atwood): automated data cropping
  • Monitoring data transfer flow from DLS to Soton.
  • ...

3. New Management at SCD/STFC

  • New member of sftaff at University of Manchester proposed July 2018-August 2020
  • Restructure at SCD/STFC for management
    • Link with Barbara Montanara https://www.scd.stfc.ac.uk/Pages/Barbara-Montanari.aspx
    • Link with Martyn Winn https://www.scd.stfc.ac.uk/Pages/Martyn-Winn.aspx
  • So we will have a core group in Manchester (Lab based) and a core group in RAL (facility based - DLS/ISIS/...)
  • Proposed integration of a Virtual development team to include Parmesh Gajjar, Nichola Wadeson etc to be invited collaborate / use funds etc.

4. AOB

  • International Review for CoSeC
  • Add software fellows to Working Group list as associate members: Parmesh Gajjar (Manchester, CCPi) and Richard Brown (UCL, CCPPETMR)...

Points Raised with more details: from November 2017 meeting:

Visitors/Fellowships awarded:

  • Hamish Carr - 8 February 2018 - Segmentation code (Presentation at RAL): Outcome: software to be integrated with CIL.
  • Joan Duran - 30 January-2 February 2018 - Image enhancement algorithms: (Presentation at RAL and UoM? ): Outcome: software to be integrated with Flagship.
  • Jim Nagy, from Emory University in the USA - 7 December 2018 - {Presentation at RAL - information mainly) link with Maths. http://www.mathcs.emory.edu/~nagy/ participant in the Isaac Newton programme "Variational methods and effective algorithms for imaging and vision" https://www.newton.ac.uk/event/vmv

Training / Seminar:

  • 6 December 2017 Training - Getting started on "Hacking" a Nikon X-ray CT system through IPC: Outcome summer presenattion and future courses to be planned.
  • 13 December 2017 MXIF Lunch-and-learn for CIL CCPi event 12noon with pizza
  • Short joint code sprint - March 2018 at RAL
  • 17 January 2018 Updates and impact on Facilities of the EPSRC X-Ray CT Tomography Roadmap http://www.ccpi.ac.uk/node/362
  • 18 January 2018 Software show-and-tell for TomViz (from kitware Inc.) tomography processing and visualisation: moving from electron tomography to XCT and neutron tomography
  • 22 January 2018 Bath/RAL Numerical Analysis Day https://www.ccpi.ac.uk/node/380
  • .... UK-USA collaboration on TomViz work Workshop to prepare for.
  • 8 March 2018, Manchester Inverse Imaging Group Seminar: Alan Turing Building, Frank Adams 2 at 2pm Prof Bill Lionheart "Histotomography"
  • Regular Manchester Avizo courses; 4-5 Dec 2017; 6-7 March 2018;

Future Ideas/Invitations:

  • NPL to talk at Manchester - 8 May 2018 ACCEPTED
  • Flagship workshop: Matthias (Cambridge) and Simon Arridge or Marta Betcke (both UCL). Also invite someone from CWI.
  • Invite ASTRA to UK : "CWI it would be most useful to have the main ASTRA developer Willem Jan Palenstijn"
  • ... or/and Joost Batenburg (COST plans)
  • PETMR - Matthias Erhhardt from Cambridge. Make interested in multichannel tomography.
  • ... also PETMR Flagship developer (Kinetic PETMR reconstruction)
  • UK-US channel, we could consider inviting Emil Sidky from Chicago
  • Sophia to come and give a talk on her work at CWI
  • ... Nick Brierley (the-MTC) invited to Manchester October 2018 ACCEPTED
  • CCPi joint workshop EY/PW on various modes - see possibly Fringe event of CECAM 2019 event
  • Bath presentation (joint NPL project)
  • ...
  • Fellowship Llion Evans to be invited to Fringe: ACCEPTED
  • Martyn Winn invited to Fringe
  • CCPPETMR Richard invited to Fringe
  • ...

More ideas welcome ...

  • Fringe meeting for Advances in Xray Imaging Workshop - ideas of topics welcome.
  • 17-19 January code sharing and 5-7 March 2018 Joint Code Sprint at RAL for CIL-Flagship single and multichannel framework reconstruction.

Case Studies:

  • "CCP Chairs to pass on existing case studies" note need for International Review of CCPs in Summer 2018
  • PE activities
  • beam hardening
  • quantifucationn - porosity
  • parts of CIL
  • ULTRA integration

Other items

  • 6 December 2017 - Flagship-IMAT meeting in RAL to update on progress.
  • Flagship-CIL code-sprint 5-8 March 2018 - plan to repeat.
  • 12 December 2017 EPSRC XCT Tomography Equipment Roadmap, Townhall Meeting (Manchester) https://www.epsrc.ac.uk/newsevents/news/capitalroadmapforx-raycomputedtomography-epsrcusersurvey/
  • 29 January - 9 February 2018 ISO / TC 213 WG10 standards meeting at BSI (389 Chiswick High Road, London E4 4AL). In the first week, Monday and Tuesday 9am-12noon XCT general topics; and Wednesday 3pm-5:30pm & Friday 9am-11:30am ISO Cttee deliberations.

Appendix A: details of events November 2017 - May 2018

Email list (CCPI-MEMBERS@JISCMAIL.AC.UK) has 378 subscribers; 13 new members since December 2017

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CCPi Exec and Working Group meeting 15 November 2017

Agenda 10:30am coffee - meeting 11am-2pm including Lunch

Flagship meeting is afterwards from 2pm-3pm http://www.ccpi.ac.uk/Flagship

Aim of the meeting: strategic positioning for next one/two year’s time - so that we have the current and upcoming one/two plan ready for future grants and networks.

Network targets: # of people / projects impact items

What kind of the bids: we should be preparing, in terms of best impacts


Agenda

Coffee from 10:30am:

Session 1:

  • (30 mins) Minutes and Actions (see list below)
  • (30 mins) CoSeC Updates
    • Licensing – SN/MT (5mins)
    • CIL Work plan and priorities -- SN/EP (15mins)
      • Brian Bray – SN
      • Mark Basham – SAVU updates + Survos + users (5mins)
    • Case Study: (10mins)
      • Segmentation using simpleflex – EP
      • Root dataset with missing projections – Genoveva/SN
  • (5 mins) Events and Training Updates
  • (10 mins) FISTA Reconstruction – EP/Daniil
  • (15 mins) CCPi Flagship Update – Daniil/Jacob

Lunch:

Session 2:

  • (15 mins) Pre-processing Imaging techniques (Nghia Vo)
  • (15 mins) Thomas Blumensath, Southampton University (TB)
  • (15 mins) Paul Quinn – DLS I14 new techniques and Updates
  • (5 mins) US/UK collaboration update (MT)
  • (10 mins) actions + further discussion
  • AOB

ACTIONS from Minutes from Last Meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20170612_0.pdf

  • ONGOING Assign name to tasks for CCPi actions and milestones (SN)
  • DONE - MT to get timetable from EPSRC for the MRF for PW
  • DONE - PW to provide contact information to NV for users on I13 with image processing issues.
  • DONE - Submit ParaView paper to EGUK (MT) also paper accepted on 12 DOF input devices for Tomography.
  • DONE - Monitor upcoming workshops/events. MT
  • PARTIAL (included UK-USA collaboration) Further visiting fellows suggestions All
  • PARTIAL Request additional codes to include in CCPi quantification software All NOTE DO NEED MORE
  • DONE Drishti-Prayog user guide:- https://www.ccpi.ac.uk/node/333
  • PARTIAL Arrange talks on Savu, IMAT and Avizo frameworks (SN) CIL talks now but can ask MB talking at WG meeting, GB to give an update
  • DONE Encourage people to add data sets to Zenodo. and Seek ISIS IMAT data to publish on Zenodo site. SN And should do Mobile Phone? https://doi.org/10.5281/zenodo.825925
  • ONGOING Case studies on beam hardening, quantification RF/SN.
  • ONGOING Arrange visit by Astra developers MB (SN) to contact MB.
  • DONE Brian Bay contacted to see how DVC code can be included CCPi quantification software (CIL) Follow on action to ask WG for user engagement cases.
  • ...
  • TODO GD and BL to discuss editing new Phil Trans issue on reconstruction. GD/BL BL putting together a list (October 2017).
  • TODO Updated proposal for joint CCPi/CCP workshop MT/BL/KT ON HOLD

Future Activities and requests for funds:

  • Update on a CPC paper proposal for 2019
  • Avizo-Amira update on project collaborations
  • Nick Brierley - MTC group - project: software-show-and-tell for 2018
  • Proposed visit - Paul Bills (Hudds)
  • Workshop Support; February 2018 a 1 day event for 20-30 UK people to meet who contribute to the ParaFEM software - linked to image-based modelling. (Lee Margetts) Request 1k for food and visiits regarding CT priorities.
  • Support Townhall meetings EPSRC Roadmap in December/ January and February 2017-2018

  • Stand and support XCT user group at NPL plus dimension XCT at Nottingham
  • Support ToScA 2018 at WMG (ToScA USA is planned for 2019)
  • Exchange Programme: UK-USA project dissemination
  • Exchange Programme: IMAT / ISIS data capture and uploaded to public space with license: add further datasets
  • Exchange Programme: New proposal by DK submitted: request funds for international speaker Dr. Joan Duran
  • Training courses update: Nikon Hacking session (Course setup by Parmesh Gajjar - request travel funds)
  • Training courses update: Tomviz - software show-and-tell day (Setup course in January if users - request summer student)
  • BSI Standards update and EPSRC Roadmap - continual reader status involvement
  • Publications: EGUK paper x2 in 2017 - repeat for 2018 in Swansea
  • Publications: CCPi-CIL Poster at ToScA - repeat for 2018 for release v1.0
  • Grants Submitted: EU COST project, 7 September 2017 (April 2018) EPSRC UK-USA collaboration, August 2017
  • ...

Items from Exec Meeting (October 2017) to take forward: created a Weekly tech meeting on Monday – 3:30pm for the Core CCPi and MT to focus on impact items.

  • PW has proposed that the core team should prepare at least one User case study for each component of the CIL
  • Prepare the "work"-plan for CCPi “Development and Engagement Plans”
  • EP informed that he is working with Robert Atwood in getting data to segmentation with CIL and would be writing this work as part of a User case study report
  • A decision has to be made about what type of software licensing under which CIL code should be released
  • Parmesh Gajjar wanting to setup a training session for “Nikon machine hacking”
  • MT has mentioned collaboration with Nick Brierley in MTC group
  • PW to link up EP with Jacob on sparse beads paper (DONE)
  • MT to write a summary for SCD newsletter on CCPi activities
    • other SCD newsletter items; regius at UoM, and 'meet the scientist' RAL day

General request for new videos and images uploaded and screencapture examples as well as zenodo items (including IMAT https://zenodo.org/record/825926)

CCPi Flagship session: 2pm-3:30pm

Items:

Appendix A: details of events June 2016 - October 2017

Main Meetings:

  • ToScA 6-8 September 2017
  • dXCT 13 July 2017 (150 att)
  • Techy RAL session plus Fringe event: 13 June 2017 and 12 June 2017

Email list (CCPI-MEMBERS@JISCMAIL.AC.UK) has 369 subscribers; 45 new members since July 2017

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  41. kunyan.callaghan@
  42. cdavidowen@
  43. biao.cai@M
  44. timothy.burnett@
  45. joseph.carter-3@

Appendix B: SLA/CoSeC report

Approval of past six months activities.

Report linked CCPisub_SP_Nov2017.pdf

CCPi Exec and Working Group meeting June 2017

Atlas Visualisation Facility: Monday 12 June 2017 - registration at:

There will be video conferencing available: https://bluejeans.com/576183356/

Draft Agenda: 10:30 coffee (for 15) arrives, Meeting from 11am-1pm

  • Approval of past six months activities (SN)
  • Exchanges
    • Short presentation on Drishti-Prayog guide (SN/EY) update (MT)
    • Fellowships including link and first images from IMAT - ICAL/Brum/Oxford etc (SN)
      • addition scan at DLS of BSI 4/4/1 samples
    • CCPi have letters of support for fellowship applications; EPSRC Manufacturing Fellowship/ EPSRC RSE II x2 / Ser Cymru Fellowship; and a tomiz.org proposal with kitware - to maintain developers.
    • EU COST links and future proposal (19 June 2017) OC-2016-2-21631 'Tomography Across Modalities and Scales'
  • Flagship update (DK/JJ)
  • Software plan / coding milestones (SN)
  • New actions / milestones
  • Web-site
  • Future meetings dXCT - NPL/BSI @WMG and ToScA @Portsmouth
  • Update from 'sister' CCPPETMR network (KT)
  • Short Talks:
    • Nghio Vo (DLS)
    • Srikanth Nagella - CIL (CCPi Core)
  • Review mid-term forecast targets
  • AOB:
    • Data transfer, "results from the RAL perfSONAR host to Manchester are around 3 Gbps and about 5 Gbps inbound to RAL"
    • Image / vidoe archive on website inc Flagship pics
    • ...

Minutes for last meeting: https://www.ccpi.ac.uk/sites/www.ccpi.ac.uk/files/uploaded_documents/CCPI_working_group_Minutes20161121.pdf

Combined Presentation: CCPiJune2017WG_c.pdf

Lunchtime 1pm-2pm Food (for 22) with a demonstration of Volume/Surface Tomography Visualisation with VR - Unity software.

  • Adative manufacturing - discussion - side meeting with Mike Curtuis-Rouse: 1pm
  • ISIS / IMAT - next stage - side meeting with Genoveva Burca: 2pm

Fringe Agenda: 2:30pm-5pm

  • The Future of XCT - 'unusual' code solutions
    • Flagship grant for Multi Channel CT and missing wedge/ poor data reconstruction (DK/JJ)
    • Sam Cooper, TauFactor tomography tool to calculate toruosity factor, volume fractions, etc
    • Darren Batey, Beamline I13, Diamond Light Source ‘Ptychography: Looking beyond the lens’
    • Tim Burnett, Henry Moseley X-ray Imaging Facility, University of Manchester ‘Multiscale 3D microstructure analysis with site specific targeting through correlation of X-ray CT and FIB-SEM serial sectioning'
    • Andy King, Soleil 'Combining tomography and diffraction at the PSICHE beamline, SOLEIL'
    • Margie Olbinado, ID19, ESRF ‘Million frames per second hard X-ray phase contrast imaging using synchrotron
  • The EPSRC XCT Roadmap outline and discussion (MT lead)
    • link to BSI standards
    • what would you do "future vision"
      • "supporting suitable and well rationalised technique-based roadmaps e.g. NMR spectroscopy..."
      • "current UK capital infrastructure ... which in turn may lead to more and/or better equipment sharing"
      • "... will have community buy-in; demonstrated through applicants taking it into consideration"
  • Unusual events as well as Coffee and Tea from 2:30pm (for 22).

Links: current EPSRC equipment Roadmap:

https://www.epsrc.ac.uk/research/ourportfolio/themes/researchinfrastructure/strategy/equipmentroadmaps/

Networking and Funding Activities: December 2016 - May 2017

  • There have been three European visitor exchanges: 12-13 June 2017 - Andy King, Asa Barber and Margie Olbinado; and November 2016 at DTI visit - CCPi lunch for four (host B. Lionheart) with Soren Schmidt, Markus Strobl, Morten Sales
  • One lab based exchange, Russell Garwood (IMAT-ICAL): 19 May 2017 IMAT/ISIS test tomography; Manchester Museum artefacts.
  • Four Seminars:
    • 14-15 December 2016 Computing Insight UK 2016 http://www.stfc.ac.uk/ciuk over 250 delegates and suppliers present - Tomo-vis talk given
    • 9-12 January 2017 Workshop in Switzerland focused on the visualisation of complex imaging: https://indico.psi.ch/conferenceProgram.py?confId=4840 Reconstruction techniques for 4D data; Multidimensional image processing with special interest on time evolving data; Visualization techniques for multidimensional data; How can the large scale research facility users benefit from advanced analysis and visualization techniques
    • 31 January 2017 Software Show-and-Tell 2pm in the RAL Atlas Visualisation Facility: Mark Basham et al., SuRVoS (Super-Region Volume Segmentation) Workbench is a new software for semi-automated segmentation of 3D image volumes. It has been developed jointly between the University of Nottingham, UK and Diamond Light Source, UK and is open source: https://diamondlightsource.github.io/SuRVoS/
    • SCD/STFC CCP Seminar, 9 February 2017; 2pm (Room S44 / R89) - Hamish Carr, University of Leeds on 'Countour tree and how it can be used for image analysis - scalability will be discussed for a system that can be tightly coupled with data analysis'
  • Three exhibitions:
    • 4-18 November 2016 Supercomputing Videos and interactive volume visualisation system at Hartree Centre stand #1137:
    • Regius Professor in Materials event for 150 invited guests at Manchester, April 2017
    • Public Engagement: MRI touchscreen datasets and images on display at British Science Week 13 March 2017
  • Training:
    • 8 Avizo courses at Manchester (6&7 December 2016; 26 January, 18 April, 19 April, 25 May and 13&14 June 2017)
    • CCPi topics course at RAL, 13 December 2016 Analytic Visualisation Features: CCPi Topics - Reading (Diamond nexus) data and scripts to python and quantification algorithms.
    • Workshop on !SuRVoS (Super-Region Volume Segmentation) - high-level algorithms for feature detection, and super-region building for smarter, quicker segmentation and analysis: at Diamond Light Source on May 4-5 2017
    • CCPi sponsored an EGU course, 25 April 2017 "3D and 4D imaging: Automation of data analysis" Jose Godinho http://meetingorganizer.copernicus.org/EGU2017/session/25578
  • BSI Standards involvement:
  • Developers' days:
    • 20 March 2017 pre-Flagship meeting at RAL and 11 May 2017 telephone-conf update.
  • Papers etc:
    • Video usage on CCPi youtube channel in total is: 8,299 (51+63+67+81+109+251+7109+338+230) and 19 touchscreen examples exist (1x cfd, 10x3d models, 6xvideos, 2xmri models).
    • Data sets on archive: (one on dropbox - needs moving to zenodo); (new sparse-dataset; and two new links from Llion Evans)

Continual CCPi support for the three annual events:

  1. 13 June 2017 "Advances in X-ray Imaging" Workshop in RAL - CCPi Sponsored with RCaH https://advances-in-x-ray-imaging-ii.eventbrite.co.uk
  2. Dimensional X-ray Computed Tomography Conference, 13 July 2017 at Warwick http://www2.warwick.ac.uk/fac/sci/wmg/research/pe/ct/events
  3. ToScA 2017 (6-8 September) the 5th annual Tomography for Scientific Advancement symposium addressing hard and soft tissue imaging, understanding materials in 3D, recent advances in hardware and software, and a broad range of applications in tomography www.rms.org.uk/tosca2017

Coding Milestones : December 2016 - May 2017

Possible Future Actions - from meeting outcomes June 2017

Items:

  • CIL code from Nghia Vo (Action SN to arrange meetings)
  • Trip for Russell Garwood to meet ISIS/IMAT (Action MT to coordinate) also meet DK regarding flgship rtest data sets

Appendix C: details of events December 2016 - May 2017

Email list (CCPI-MEMBERS@JISCMAIL.AC.UK) has 326 subscribers; 25 new members since December 2016 (plus 21 in June 2017, so far)

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CCPi Exec and Working Group meeting November 2016

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
    • Short presentation on Helical Activity (BL)
    • Short presentation on Drishti-Prayog guide (SN/EY)
  • Software plan / coding milestones (SN)
  • New actions / milestones
  • Web-site
  • Future meetings
  • Short Talks:
    • Automated Testing Service Presentation - current work and future possibilities (RF)
    • Update on Beam Hardening (RF)
    • Update from CCP WSI organisation - fluid flow development (RF)
  • AOB
    • Advanced Radiotherapy Network+: Sandpits and PhD studentships

Extras:

  • CCPi for software integration
  • Testing Service for CCPi code
  • Proposed Summer school in Tomo at Bath 2017
  • DTI visit - lunch, Prof Soren Schmidt, Prof Markus Strobl, Dr Morten Sales with Prof Bill Lionheart (November 2016)
  • Support for "short course /workshop as part of EGU2017. The subject would be automation of image analysis from large datasets using freeware. Probably I would focus on using imageJ."Jose Godinho
  • Daniil "just found a very fresh paper from C. Bouman's group where they are trying to use some interesting hardware elements to significantly accelerate model-based iterative methods. https://engineering.purdue.edu/~bouman/publications/orig-pdf/PPoPP-2016.pdf

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 - KNL)
  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
  • 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

  • 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 12 attendees
  • 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@

Roadmap and standards

Reminder and FYI the CCPi (tomographic Imaging) has a user list of about 330 people and slowly growing – and other community XCT lists exist; NPL’s and ToScA? ’s with NHM for example; so this is timely. My initial document from this proposal listed numerous technologies rising from the XCT development – that are beyond simple scale quantification; including (multi-scale) imaging analysis and other derived; chemistry, stress etc processes.

I see two main outcomes in the UK;

  • 1. simpler imaging systems - similar to the development of SEM where cheaper lab based facilities with a kite-mark of standardisation are affordable to all groups (<50K), and installed with Guides of Practice to 100's of groups within the UK from small university research labs to SME manufacturing facilities.
  • and 2. high-end very fast and multi-channel/energy imaging systems - creating large data deluge that allow multiple parameters to be recorded at once and continually giving physics, biology, chemistry and engineering values for sub/global-parts of an object under multitude types of influence (different environment in-situ rigs); changing temperature, pressure, shearing, catalytic reaction etc.

So many places will have one or a few systems and some will have a multitude of systems – over many scales/ (in-situ)rigs / and all being 4D or 5D (temporal etc) and thus becoming bid data problems.




Old Items:

CCPi Core Developer's Items

Agenda 15 September 2015:

Comments on PET-MR: framework code discussion.

- CCPi activity: Quantification workshop in the Autumn - use ToScA? group:- ACTION MT (Sri / Ron / Trintan)

BoneJ? / Rootrak / FEI system (Remi - Action MT to find out when in November and at Brum) / ...

Segmentation needs - Invite list. MT to coordinate: CCPi list: and ToScA? community (ACTION MT and SRI). PW to give contact in copenhagen

- Carousel built RCaH? - Matthew and Loic - optimised for rock. Data capture done:- calibration.

- CCPi Code Development Updates:

1. Update on 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. Available in UoM? but need extended users.

>> Tristan (and Russel) for direct transaction. ACTION Sri

>> SCARF reconstruction:

>>

Rob Bradley: reader for Zeiss for CCPi code as well as XTek etc (Joint action with tristan Sri below)

2. Update on Quantitative visualisation algorithms: work in quantification and the new Avizo algorithms have been expended:

- contributions by Erwan Plougonven,

>> UoM? then CCPi list

- extra code from Robert Bradley (MXIF)

>>

- and a study on beam hardening code (Queen Mary).

>>

3. Update on frameworks:

- Diamond framework savu at DLS

>> Ask Nicola work on presentation: ACTION MT. Multispectral analysis, see BL below.

- ISIS IMAT framework

>> switch on this week:

- Stand-alone Avizo framework at UoM?

>> Ali replacement: Tristan, contact. ACTION Sri

- Case studies required: Action MT to send form around EPSRC form.

>>

- Update on fellowships and links to developers:

Inc. Nicola Wadeson now in DLS; and developers at ISIS/IMAT (as well as management from Erica Yang)

>> Manuch :-

- Infrastructure:

1. Data store: setup on the zenodo website https://zenodo.org/collection/user-ccpi?ln=en

Update with touchscreen items (link to ICAL Russell Garwood).

2. Youtube site update with videos (from above)

3. CCP website update

4. New data transfer service from DLS to UoM? etc

Also test to new ICAL machine (sponsored by STFC)

5. Link to a ToScA? newsletter list etc

>>

- Outreach/Networking:

1. MOSI event end of October (Saturday 31 Oct)

2. EU COST events: intro2015 in November

3. DL open day in 2016

- Publications:

1. New Phil Trans issue with Manuch Solemani: bully >> link to

- Future Events:

1. Rerun of EPSRC SLA user needs survey: October 2015

2. Training and developer's days are to continue as normal

3. The next "away-day" developers’ day is proposed to be at the Warwick University Manufacturing group

4. Future software show-and-tell events will be based on the suppliers and three Frameworks

- Bids:

1. Outreach events via Phil Manning (ICAL) STFC grants available

2. Update from Bill Lionheart and others from developers day

CCPi and CCP MR-PET for 2015-2016

From the developers;' day (att 8). Code from STIR stir.soureforge.net STIR system needs updating - PET/SPECT code is available under the L esser GPL for libs: otherwise it is GPL but may move to Apache License. The size and performance is key with 600 x 60 rings giving 200-400m events resulting in a final volume size of about 200 cubed. Main issues are noise due to a lots of random events and scatter, about snr. Separate parts could be optimised/parallised; regulariser could be improved etc. constrained optimiser (LGFBF). Future work needs to consider:

  1. MPI/Open-MP/GPU (lots of race conditions)
  2. Matlab interface
  3. memory management to be improved esp for 3D data
  4. rotation based optimisation

Aside: Slicer 3D includes a module for Radio Therapy Planning (SlicerRT? ) which is possbly relevant, e.g. http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT

slicerRT is more possibly more about the "quantification" of the processed data while the stir project is more about the reconstruction methods.



January 6, 2015 - CCP SP Chair reports:

ChairReportJanuary2015

ChairReportJune2015

ChairReportDecember2015

SLA Summary Report January 2015

SLACombinedReport



Items 2015-2016

  • 2 Feb - 1 May 2015: Visiting Scholar, Noicola Wadeson: signed contract

Past CCPi activities: Compressed Sensing: funding from from Soton (Thomas Blumensath):

  • Nikon metrology / EPSRC for an EngD? student in "x-ray ct reconstruction uncertainty"
  • EPSRC Doctoral training centre studentship on "nonlinear x-ray reconstruction"
  • A KTS with AWE on reduced angular access reconstruction
  • A TSB grant with Qinetiq, Nikon metrology, AxiTek? , UCL, RR on "laminar CT reconstruction"

Collaborations:

  • Talk on Compressed Sensing and tomography at the "Sparse Tomo Days" at DTU Denmark 2013/2014.
  • Industrial collaboration with; The Welding Institute (TWI), The National Physical Laboratory, The British Standards Institute, Nikon Metrology and The Atomic Weapons Establishment.
  • Jared Tanner and Thomas Blumensath are organising a special session on "Compressed Sensing" at this years "Inverse Problems" conference IPTA2014

Summary Report June 2014 and plans for 2015

CCPi

The project is proceeding as planned with support from Barry Searle, now joined by Srikanth Nagella and Ronald Fowler, who are based at RAL. Due to the sudden loss of David Worth from the team there has been an effective under-allocation which will be corrected in 2014-2015 (see below).

Administration: Working group meetings were organised during Q2 and Q4 2013: A series of developers workshop have been held on 14th Jan and 20th May in Birmingham with the next meeting already planned for 22 July at Nottingham. We are also assisting in the first and next Tomography for Scientific Advancement symposium (ToScA? ) meeting in the Natural History Museum (Sep 2013 and 2014). A monthly showcase involving eight short software show-and-tells were organised at RAL during this year and will continue.

Contact has been established between CCPi and CCP-ASEArch. A CCPi Seminar was held Nov 2013 including a joint presentation from Lucian Anton and Jonathan Hogg of CCP-ASEArch on GPUs and their work developing algorithms for that architecture. It was a video conference between DL and RAL and around 35 people attended. Work has started on looking at 4D iterative reconstruction algorithms. Then in January we agreed on a project managed by the CCPi Flagship project team that has now started in April 2014 (this is described in the CCP-ASEArch section of the Technical Appendix workplan.

Development targets met:

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

Metrics 2013/4 need values for 2014/5

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

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

NEED metrics for CCPi.



Technical Appendix 2014 and plans for 2015

CCPi – Tomographic Imaging

Non destructive 3D X-ray imaging is becoming increasingly important in many areas of science and its application to Energy, Healthcare and Security. For example it is having a dramatic impact on fields as diverse as security (e.g. baggage and body scanning at airports and screening of vehicles at ports), engineering (e.g. visualising stress corrosion cracking in nuclear plant and the degradation of fuel cells) and medicine (e.g. cancer treatment and artificial tissue engineering). The spatial and temporal resolutions are increasing dramatically. RC funded synchrotron sources are rapidly increasing the numbers of x-ray imaging instruments available (the European Synchrotron Radiation Facility (ESRF) now has 10 beamlines, Diamond Light Source (DLS) is currently building 4 new imaging beamlines). Laboratory x-ray imaging facilities are becoming increasingly widespread. This expansion is mirrored elsewhere with the global CT market now worth $150M (+ $5B in medical CT) both expanding at 10% pa , while 30% of the data stored on the world's computers are now medical images. Unsurprisingly, papers on x-ray tomography have also increased sharply this decade (doubling every 3 years with 1,500 published last year).

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

Outline of Proposed Core Support Activities:

Most people who acquire and analyse X-ray images have little or no knowledge of X-ray tomography reconstruction and analysis, consequently the involvement of the Core Support is critical if we are to achieve a significant step jump in the level of information obtained by UK science from X-ray imaging. As well as administrative support for the CCP (organization of working group meetings, maintenance of web sites), the core support team (1.5 FTE per annum) at DL will:

  • Standardise input and output data formats;
  • Standardise software coding rules and testing;
  • Assist with porting, parallelisation and optimisation on different hardware platforms including novel architecture systems.
  • Provide centralised distribution and controlled releases for software;
  • Provide installation user support for software, and run workshops/training events;
  • Collate and distribute existing algorithms and code, including licensing requests;
  • Encourage CCP participants to make their algorithms and code available;
  • Create a gallery of test real x-ray image test object datasets for mathematicians to test and benchmark new algorithms; and
  • Maintain documentation.

This project aims to provide toolboxes for both 3D image reconstruction and 3D image analysis algorithms. In simple terms it is estimated that the project requires 0.5FTE for maintaining network, website, running workshops and training course, benchmarking, licensing issues etc; 0.5FTE for developing and maintaining the 3D image analysis toolbox, 0.5FTE for developing and maintaining the image reconstruction toolbox.

CCPi Milestone Date

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

Task Effort Including Underspend

  • Additional Overall Coordination 0.2 (Turner)
  • Maintaining network, website, running workshops and training course, benchmarking, licencing issues 0.5
  • Developing and maintaining the 3D image analysis toolbox 0.5
  • Developing and maintaining the image reconstruction toolbox 0.5
  • Evaluation of neutron imaging software 0.25 (Yang)

Total 1.5 FTEs carried ovcer underspend 0.45 FTE

Staffing Effort including Underspend

  • Martin Turner 0.2
  • Barry Searle 0.6
  • Srikanth Nagella 0.6
  • Ron Fowler 0.3
  • Erica Yang 0.25

Total 1.5 + 0.45






CCPi Working Group Meeting December 2014

Agenda (so far):

- Actions from last meeting

- Report on core support activities/plans (BS[MT]/RF/SN)

- Report on flagship grant (DK)

- Framework Reviews There appears to be three frameworks that we need to consider and understand:

- Diamond's DAWN framework that is being redefined (MB)

- ISIS (IMAT beamline) framework that links to parts from DAWN and being put together (SN)

- The CCPi code can link to these (above) and being tested also as stand alone executable ()

- Test datasets ()

- Phil Trans Journal status (MS)

- Visiting Fellowships

- Videos (outreach) and TouchTable? for Volume Vis

- EU updates (BL)

- CCP renewal call

- Other calls and projects

- AOB

The last draft minutes are available at:

http://www.ccpi.ac.uk/minutes.shtml

CCPi Phase 2 Objectives

The new EPSRC proposal for CCPs is due on 7 October 2014 Key next stage progress items for the community are:

  • Include Neutron Tomography - link with ISIS IMAT bamline
  • Further close collaboration with DLS tomography and use outside of the national facilities
  • Code replacement for black-box reconstructions currently within lab based systems
  • Include Impedence Tomography - links also with ..
  • ... multimodality operations

Increase use and functionality of the reconstrcution and quantification toolkits currently available. Consider further dataflow and linking together tools.

ACTIONS We need to submit to SCD (STFC) [to discuss with Paul Sherwood] an outline workplan - one page or two: IN TWO WEEKS TIME (19 September 2014)

  • What code needs to be defined / updated
  • Very general milestones - covering mainly first year of the five year plan
  • Amount of SLA support requested - could expand from 1.5FTE to 2.0FTE
  • Type of support - can state need experience / links to facilities

ACTIONS Final submission is only one JeS? for the CCPi Mark2 - DUE 7 OCTOBER 2014

Introductory Text:

Non destructive 3D X-ray imaging is becoming increasingly important in many areas of science and its application to Energy, Healthcare and Security. For example it is having a dramatic impact on fields as diverse as security (e.g. baggage and body scanning at airports and screening of vehicles at ports), engineering (e.g. visualising stress corrosion cracking in nuclear plant and the degradation of fuel cells) and medicine (e.g. cancer treatment and artificial tissue engineering). The spatial and temporal resolutions are increasing dramatically. RC funded synchrotron sources are rapidly increasing the numbers of x-ray imaging instruments available (the European Synchrotron Radiation Facility (ESRF) now has 10 beamlines, Diamond Light Source (DLS) is currently building 4 new imaging beamlines). Laboratory x-ray imaging facilities are becoming increasingly widespread. This expansion is mirrored elsewhere with the global CT market now worth $150M (+ $5B in medical CT) both expanding at 10% pa , while 30% of the data stored on the world's computers are now medical images. Unsurprisingly, papers on x-ray tomography have also increased sharply this decade (doubling every 3 years with 1,500 published last year).

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

Outline of Proposed Core Support Activities:

Most people who acquire and analyse X-ray images have little or no knowledge of X-ray tomography reconstruction and analysis, consequently the involvement of the Core Support is critical if we are to achieve a significant step jump in the level of information obtained by UK science from X-ray imaging. As well as administrative support for the CCP (organization of working group meetings, maintenance of web sites), the core support team (1.5 FTE per annum) at DL will:

  • Standardise input and output data formats;
  • Standardise software coding rules and testing;
  • Assist with porting, parallelisation and optimisation on different hardware platforms including novel architecture systems.
  • Provide centralised distribution and controlled releases for software;
  • Provide installation user support for software, and run workshops/training events;
  • Collate and distribute existing algorithms and code, including licensing requests;
  • Encourage CCP participants to make their algorithms and code available;
  • Create a gallery of test real x-ray image test object datasets for mathematicians to test and benchmark new algorithms; and
  • Maintain documentation.

This project aims to provide toolboxes for both 3D image reconstruction and 3D image analysis algorithms. In simple terms it is estimated that the project requires 0.5FTE for maintaining network, website, running workshops and training course, benchmarking, licensing issues etc; 0.5FTE for developing and maintaining the 3D image analysis toolbox, 0.5FTE for developing and maintaining the image reconstruction toolbox.

Project; SLA Milestones

Short Report 2013-2014:

The project is proceeding as planned with support from Barry Searle and now Srikanth Nagella and Ronald Fowler at the agreed project levels; but the levels have been drastically effected by the abrupt removal of a member of staff in this period. This meant in the year 2013-2014 there has been an effective under-allocation so targets will be slightly changed to 2014-2015.

Administration: Organise working group meeting Q2 and Q4 2013: All meetings have been organised although the level of service is being improved. A series of developers workshop have been held on 14th Jan and 20th May in Birmingham with the next meeting already planned for 22 Jul at Nottingham; we are also assisting in the first and next Tomography for Scientific Advancement symposium (ToScA) meeting in the Natural History Museum (Sep 2013 and 2014). A monthly showcase involving eight short software show-and-tells were organised in RAL during this year and will continue.

Contact has been established between CCPi and CCPASEArch, a CCPi Seminar was held Nov 2013 including a joint presentation from Lucian Anton and Jonathan Hogg of CCPASEArch on GPUs and their work developing algorithms for that architecture. It was a video conference between DL and RAL and around 35 people attended. Work has started on looking at 4D iterative reconstruction algorithms. Then in January we agreed on a project managed by the CCPi Flagship project that has now started in April 2014.

Proposed workload: Collaboration with Eugeny is in progress. 1. Using test data that Daniil Kazantsev generated. 2. After his reconstructions are done we will compare his method with conventional tools that DK uses and write a report.

Development targets met:

  1. Initial particle tracking code based on MXIF is complete and in use. Modifications will be made to generalise function to determine proximity of particles from one form to the next.
  2. We are implementing histogram based thresholding methods including those from ITK, and further tools are ongoing.
  3. Iterative reconstruction development proceeds; we have completed a !NeXus reader for Diamond Light Source data sets; and have run test Diamond data sets on the Hartree Centre !ScaleMP node (order 1TB RAM), where iterative methods require about 20hrs/iteration. The code has been modified to reduce memory requirements for workstations and for the following stage required optimisation to reduce compute cost per iteration which is currently ongoing.
  4. The external profile of the project has been raised by updating the CCPi website and creating a dedicated CCPi YouTube channel http://www.youtube.com/channel/UCGB578xcyXNQyiBsufEFIeQ
  5. Modify CGLS code to analyse example Diamond data set complete by Q3 2013.
  6. Optimise projection algorithm at core of iterative routines for an accelerated architecture (GPU/Phi) Q1 2014. The optimised Diamond version has been tested on Xeon Phi and further work tests will occur as part of the ongoing optimisation.
  7. Add 2 new iterative reconstruction algorithms from network members or flagship project to reconstruction suite Q1 2014. at a developers' meeting in Manchester in March it was discussed how the developer/flagship PDRA should integrate their algorithms into the ccpforge archive and a way forwrd is being used.

Deliverables produced:

Papers: Three papers submitted through the Flagship; “A novel technique to incorporate structural prior information into multi-modal tomographic reconstruction” accepted to “inverse Problems”: http://iopscience.iop.org/0266-5611/30/6/065004

“4D-CT reconstruction with unified spatial-temporal patch-based regularization” on second revision in “inverse Problems and Imaging” and

“Multimodal image reconstruction using supplementary structural information in total variation regularization” on second revision in “Sensing and Imaging”.

Presentations: Last year there have been;

  • Monthly software show-and-tell events from August 2013 - March 2014: eight meetings (total attendance, 113)
  • The first Software Developers' Workshops with presentations and discussions (14 January 2014 Developers' day at Birmingham; attend 14)
  • Stand at Materials KTN Materials Research Exchange (24-)25 February 2014, Ricoh Arena, Coventry. This promoted the HIP, CCPi, Hartee Centre and related facilities including ISIS. There was also a one-minute pitch "The Use of Synchrotron and Neutron Imaging within Materials Science using STFC Facilities"
  • Combined stand for CCPi and HIP at the IIP 6 November 2013. Included pull-up stand, case studies and a poster for the main CCPi activities.

Training sessions: Across Diamond / RCaH / University of Manchester Collaboration / STFC labs there have been 9 training courses (total attendance; 117) .

  • Diamond [Approx 26+19 (about 30 PhD)] 8-9 April 2014 Part of the Diamond Manchester Collaboration, CCPi and HIP, the University of Manchester and Diamond Light Source a 2 day course on the Visualisation and quantification of tomographic data; 15-17 January 2014 Avizo and CT course DLS/STFC
  • UoM [Approx 10+9] 28-29 January 2014 Avizo and CT; 29 October - 1 November 2013, Avizo and CT
  • RCaH [Approx 8+22+7+7] 27-28 January 2014 RCaH Training Course in CT and Avizo; - 9th July 2013 Manchester CT reconstruction at Diamond workshop; 7-8 October 2013, Avizo (VSG) and 12 December DVC training course by RCaH at RAL
  • RAL [Approx 9] 24-26 June 2013, Avizo (VSG)

New SLA Milestones for year: 2014-2015

  1. Organise working group meeting/ ToScA involvement, and monthly show-and-tell sessions - Ongoing
  2. Support current training courses and organise developer workshop to teach (for C++ includes; Basics of an application (Avizo, ImageJ); Programming (C++/Java) with reference to particular API; API for Avizo, VolView, ImageJ; Development with ITK; Implement a module to take away) - Q4 2014
  3. Port 3 or 4 iterative codes so that they can be compared on the same datasets - Q4 2014 (extra targets: 3.1 Tidy up of centre of rotation issues and optimisation of iterative code with Diamond NeXuS data sets for integration with DAWN. Q4 2014 and 3.2; Port of Manchester filtered back projection into NeXuS? package as anoption with DAWN - Q1 2015)
  4. Iterative code up and working for the Nikon XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work - can tackle problems with fewer images. Work with Tristan Lowe in Manchester to define a beta version (in the ccpforge) - Q2 2014 (Release data release version Q1 2015)
  5. Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in !VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3 -Q3 2014
  6. Implementation of two/three further quantification algorithms for and from the community (Extra item 7.1 Potential to support Avizo, !ImageJ and !ParaView. Note simpleITK package is supposed to allow ITK functionality to be called from Java so it might be possible to have common packaging of the algorithms) - Q3 2014

Extra Admin target to promote once complete as is in progress at Manchester with the lab based systems.

  1. Capture an idealised dataset - suggested minimum of 2048 images each comprising 8 frames so that we could for example compare reconstructing 2048 1 frame projections with 1024 (each 2 frames summed) projections with 512 (each 4 frames summed) projections with 256 (each 8 frames summed) projections. Possibly with Diamond (Mark Bashham) - Q4 2014




Reconstruction Toolkit:

The key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/cgls

Core Workplan: 0.5 FTE

Items from discussion:

  • Iterative code up and working for the Nikon XTek X-Ray CT stage. Links to Nicola Wadeson and Daniil Kazantsev work - can tackle problems with fewer images. Work with Tristan Lowe in Manchester to define a beta version (in the ccpforge). June 2014
  • Iterative code modified and working for Diamond datasets (CT stage) - code tested, published and submitted into the public domain.
  • Manchester/Diamond code - stored in repository and available for users; parallel-beam reconstruction.
  • Manchester/Diamond code - modified for cone-beam reconstruction.
  • Used code for images with a missing wedge - there is new in situ kit that will have some blind views.
  • Port 3 or 4 iterative codes so that they can be compared on the same datasets. October 2014
  • Capture an idealised dataset - suggested minimum of 2048 images each comprising 8 frames so that we could for example compare reconstructing 2048 1 frame projections with 1024 (each 2 frames summed) projections with 512 (each 4 frames summed) projections with 256 (each 8 frames summed) projections. Possibly with Diamond (Mark Bashham) July 2014

Extra Activities

Co-ordinate collaboration with CCPASEArch; ASEArch activites include work with Evgueni Ovtchinnikov commencing 1 April 2014: This work is ASEArch related and is specific to that cost code. The work involves numberical methods, to apply a multigrid solution to improve the issues caused by a gradient based regulisation coefficient, as applied to an iterative CGM (Conjugate Gradient Method) that is coordinated by the CCPi Flagship fellow, Daniil Kazantsev. These activities are in their very early stages to improve the convergence of the algorithm but requires data analysis.

EPSRC CCPi Flagship project funds Daniil Kazantsev on compressed sensing methods (iterative reconstruction) methods (has separate repository http://ccpforge.cse.rl.ac.uk/gf/project/ccpi_itr)

- Within the CCPi there are two of the funded Co-Is groups who have teams dealing with Conjugate Gradient Methods and other iterative solutions to solve these inverse problems; http://people.bath.ac.uk/ms350/ (m.soleimani@bath.ac.uk) Manuchehr Soleimani (aka Manuch) from Bath., and the second slightly larger group in Manchester is under Bill Lionheart http://www.maths.manchester.ac.uk/~bl/ (bill.lionheart@manchester.ac.uk) Will Thompson, in Manchester is on a related postdoc, (William.Thompson-2@manchester.ac.uk).

Quantification Toolkit:

The quantification toolkit involved integration of code within Avizo, VolView and possibly ImageJ (and possibly Drishti); (Note now ParaView does volume visualisation this is an option as well).

Key repository is at: http://ccpforge.cse.rl.ac.uk/gf/project/iqa/

Core Workplan: 0.5 FTE

Items from discussion:

  • Accessible volume code (originally Matlab from Sheng Yue) has been re-implemented in VolView and Avizo. There are scalability issues for up to 2000^3 to 4000^3. June 2014
  • Parallelisation and integration of a CFD code into Avizo and the integration of CCPi algorithms into other packages.
  • Implementation of two/three further quantification algorithms for and from the community December 2014
  • Algorithms awaiting publication: support to be given.
  • Potential to support Avizo, ImageJ and ParaView. Note simpleITK package is supposed to allow ITK functionality to be called from Java so it might be possible to have common packaging of the algorithms. Novemeber 2014
  • Develop a project to re-engineer an existing code for Digital Image Correlation. Q2 2014 (Work with Brian Bay (the original developer) of Oregon State University; This would be a plug-in to Avizo and ImageJ? , something novel to both applications)

Extra training:

  • Continue support for CCPi training courses given by community
  • Organise developer workshop to teach (for C++ includes; Basics of an application (Avizo, ImageJ? ); Programming (C++/Java) with reference to particular API; API for Avizo, VolView? , ImageJ? ; Development with ITK; Implement a module to take away) December 2014

Extra Activities

Ron Fowler has now taken ownership of this CCPForge archive, and an initial survey of code/updates is ongoing.

Extra activity involves data flow links through SCD (Erica Yang) links with the HIP and ISIS. New proposed projects have been constructed with intial plans.

A good initial document to review is the last years’ mid-term review for general update: http://www.ccpi.ac.uk/Documents/mid-term_report.pdf ... and the early VolView integration plan is at: https://epubs.cclrc.ac.uk/bitstream/9412/RAL-TR-2013-007.pdf

- Within the CCPi there is the funded Co-I group who have members dealing with Quantification Visualisation; http://www.rc-harwell.ac.uk/manchester-x-ray-imaging-facility under Professors Lee and Withers (peter.lee@manchester.ac.uk).

Software evaluation including: Dream.3D "very good for DCT / EBSD datasets; origin’s are Tony Rollett’s group".

Administration Items

Items to be acted upon - as well as meetings and training as below.

  • CECAM conference/workshop (possibly synergistic with COST Extrema)
  • Phil Trans Special Issue Mark 1
  • Support for CCP4Vis and future CCPi mark 2
  • Interim report in October on all CCPi targets
  • CCPi survey dissemination and use cases
  • ...

Papers etc.:

  • New method to calculate center of rotation based on the double-wedge property of Fourier transform of a sinogram. It’s on Optics Express and open access (http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-22-16-19078 ). It's a very robust method, easy to implement and has a low computational cost. I believe this is the solution for a very old and annoying problem in tomography (Nghia Vo)

Our viz/ccpi developers' days which are once every three months - attendance 12,10,14 each time.

Dates of Future Events and CCPi Management:

There is a Core 0.5 FTE management time available to support activities and manage listserv's etc.

  • Tuesday 20 May 2014 - CCPi software developers' day in Birmingham - focus of this is on reconstruction algorithms with an emphasis on DLS and the DAWN system
  • Wednesday 21 May 2014 - Celebration of Queen's Anniversary Prize for New Techniques in X-ray Imaging of Materials Critical for Power, Transport and other Key Industries , University of Manchester: 22 May
  • Friday 30 May 2014 - Tomo-and-Coffee session: proposed "dataflow session using volume vis in paraview" (RAL, 2pm)
  • Tuesday 10 June 2014 - CCP Steering Panel - only CCPi PI attending, Phil Withers, but we may need to feed details for the report into this.
  • Monday 17 June 2014 - CCPi Working Group meeting - either at RAL or DL. 6-monthly meeting.
  • Thursday 27 June 2014 - DLS reviewing their dataflow system DAWN on the RAL Tomo-and-Coffee session (2pm)
  • 22 July 2014 - CCPi software developers' day in Nottingham - visit to the new Hounsfield facility. Date to be confirmed.
  • 1-3 September 2014 - CCPi co-sponsoring, Tomography for Scientific Advancement (ToScA) Symposium in affiliation with the Royal Microscopy Society at the Natural History Museum, London, UK
  • Sponsoring through HIP: Young Researchers in Image-based Modelling 9 September 2014.

CCPi monitors/promotes various training courses including

  • Monday 8 September, Ajay Limaye is arriving at RAL to give a workshop and discussion of the features. (http://sf.anu.edu.au/Vizlab/drishti/) Latest Code: https://github.com/AjayLimaye/drishti - being held in RAL
  • 8-9 April 2014 Part of the Diamond Manchester Collaboration, CCPi and HIP, the University of Manchester and Diamond Light Source a 2 day course on the Visualisation and quantification of tomographic data. (Day 1: Introduction to X-ray Computed tomography. Avizo standard workshop. This will cover loading in data sets, image processing, segmentation and visualisation (ImageJ and Avizo) (Day 2: Introduction to Avizo Fire workshop (quantification), Analysis of inter-connected structures using Avizo and ImageJ)
  • Thursday 8 May 2014 - Aviso training - specialist session
  • June - week long session at University of Manchester
  • MXIF advanced users: How XCT instruments work: This course will cover the individual components of XCT instruments and their respective capabilities – this is essential to those who want to know how data is generated and affected under different conditions – 11 June 2014 Introduction to XCT reconstruction code. This course will explain the various reconstruction codes that are currently being applied to XCT – 12 June 2014 Advanced characterisation techniques: this course will provide the introductory knowledge regarding multi-scale imaging, correlative imaging, phase contrast and time lapse tomography – 13 June 2014
  • MXIF introductory courses: Introduction to X-ray Computed Tomography (XCT) and AVIZO standard on the 3rd June 2014. AVIZO Fire – advanced characterisation of discrete features such as precipitates using AVIZO - 4 June 2014. Analysis of interconnected structures such as complex porosity structures using AVIZO, ImageJ and MATLAB - 5 June 2014 Image based meshing course – this course will explain how to create a model mesh using ScanIP with volumes generated from AVIZO. These meshes can then be used directly in ABAQUS – 6 June 2014 (yet to be confirmed)
  • Avizo visualisation course at the Diamond House, 16-17th July 2014; via the RCaH? /Diamond Consortium

Links with EuroVis 9-13 June 2014 through the HIP exhibition.

Deliverables - Reconstruction and Quantification through the CCPi community

Main website is at: http://www.ccpi.ac.uk/

End of Project Targets

New CCP calls are due in June 2014, and the current grant EP/J010456/1 ends on 28 August 2015. Following targets are to be met or exceeded; some already have been.

Increase user base: 80 members of network; Expand to include electron and MRI imaging communities; Outreach beyond EPSRC.

International Links: 6 International Fellows Visits; 3 International contributors to algorithms

Links with Industry: 10 Company members; 10 Industrialists attend training courses/workshops

Feedback from workshops/training: 70 different people have attended training/workshops

Outreach: 9 outreach videos for schools available on youtube

New scientific functionality added: 8 analysis routines in toolbox; 4 reconstruction tools added

Ability to run on new platforms: GPU version of reconstruction code available

Flagship: new scientific functionality added: Fewer projection methods; Discrete Tomography tool with interface to finite element meshing code.

Flagship: increased efficiency of code: Fully documented iterative algorithm toolbox for mid-range cluster systems

Flagship: Ability to run on new faster platforms: Accelerator based version of iterative algorithms available

Papers: 8

Complementary follow-on funding: 2 industry funded studies and 1 RC grant

Poster with longer description:

Poster created in 2013 by Daniil Kazantsev.

ccpiposter.png

-- MartinTurner - 9 Apr 2014

Topic attachments
I Attachment Action Size Date Who Comment
jpgjpg 35thtconfcw.jpg manage 30.0 K 15 Mar 2018 - 14:34 MartinTurner  
pdfpdf CCPiJune2017WG_c.pdf manage 7186.0 K 14 Jun 2017 - 08:12 MartinTurner  
pdfpdf CCPisub_SP_Nov2017.pdf manage 601.8 K 04 Dec 2017 - 09:19 MartinTurner  
jpgjpg WP_20170612_013cw.jpg manage 53.6 K 14 Jun 2017 - 08:46 MartinTurner  
pngpng ccpiposter.png manage 1070.1 K 10 Apr 2014 - 14:30 MartinTurner  
pdfpdf cil_opti_ccpi_exec.pdf manage 126.2 K 28 Mar 2018 - 10:52 MartinTurner  
Topic revision: r142 - 12 Oct 2018 - 08:39:23 - MartinTurner
 
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