FLAGSHIP - Initial pre-kickoff meeting and CCP core integration process: plus follow-on meetings

Introductions and roles of related participants.

Conventional X-ray imaging entails a polychromatic X-ray source (i.e. with a full spectrum of energies) but with energy-indiscriminate detectors (registering a single grey-scale channel). However, technological breakthroughs in energy-sensitive detectors enable a new era of tomographic imaging in 'colours' (multiple channels).

Official EPSRC grant notification http://gow.epsrc.ac.uk/NGBOViewGrant.aspx?GrantRef=EP/P02226X/1

The CCPi SLA and the Flagship grant developers, will both have governance through the Working Group - with these meetings planned every six months (approx June and December).

  • Techy-Admin meeting started with this early meeting on 20 March 2017 at RAL RCaH (att 14 +3 remote via webex)
  • Start date is 1 April 2017 and end date is 31 March 2020
  • Next Working Group meeting is: 12 June 2017 https://www.eventbrite.co.uk/e/ccpi-working-group-meeting-tickets-32227704933
  • RSE Conference: http://rse.ac.uk/rse-conference/ 7-8 September 2017 Call for papers deadline is 28 April 2017
  • Next Techy-Admin meeting (t-conf: 11 May 2017, informal at Working Group/Fringe 12/13 June 2017, next 12 September 2017 then ...)

The aim for these exchange Techy-Admin meetings are to focus on the "user needs/outcomes" as well as the "techy/maths problems".

Original proposal diopocument: EP-P02226X-1proposalPartA.pdf and Gantt chart: EP-P02226X-1proposalPartB.pdf

From the Project Gantt chart there will be a three phase structure (colours on chart) to focus on published user impact.

  1. BLUE Algorithmic development of a specific user proble (DK, JJ)
  2. RED CCPi harding proces and integration (SN, EP, EY)
  3. GREEN User publication of outcomes with links to facilities and lab as appropriate (MB, WK, BC)

This will be repeated creating a set of beta versions etc., of the toolkit.

Presentations CCPi Flagship Grant: Phil Withers

descr2.jpg descr1.jpg

Invited External Speakers

Presentations Core CCPi development intro and updates

CCPi Flagship Management Process

CCP admin web links etc.

  • Create a tab on the main CCPi webpage
  • Use project planning tools - e.g. slack (private messaging), trello (public project outcomes) and github/ccpforge site.
  • Publicity and publications: opportunity at "Advances in X-ray Imaging" in RAL (13 June); NPL X-ray User Conference (TBA July), !ToScA (6-8 September)

Link to RSE at Manchester and community: http://rse.ac.uk/

Actions and Discussions

  • Create Good-and-Bad data sets - @ ISIS (WK and DK) @ DLS (MB and DK) and in @ Lab (JJ, RC)
  • Ring Artifact highlights: integrtae in savu version from DAWN (MB and SN)
  • Missing Wedge algorithm (SN and PG and MB) - include published / paper outcomes
  • Helical system (BL and SN) - include published / paper outcomes
  • Very Noisy Data (??)
  • Poster for Warwick Meeting with NPL standards - July 2017
  • Poster / talk at ToScA - 6-8 September 2017
  • Poster for Advances in X-ray Imaging, 12-13 June 2017 - convert to a leaflet for CCPi stand etc.
  • ...
  • Joint workshop with PETMR flagship (action MT / BL / KT) this should be an anual workshop topics to include;
    • Baysian Methods,
    • HW speed-ups and,
    • SW framework links between flagships,
    • ...
  • PETMR (SIRF https://github.com/CCPPETMR/SIRF/wiki) links and admin structure
  • Possble link to Engin-X (ISIS) Joe Kelleher to help coordinate
  • ...
  • Integrating route? (with CCPi to Savu?) / Which platform? (Python vs Matlab) / Version control (CCPForge vs Github)
  • Interaction with CCP PET/MR - annual workshop proposed
  • Join RSE team at Manchester and in SCD: including courses
  • ...
  • Summer student request to CCPi "... laminography work I'd be interested to see taken a bit further than what I think will be possible during the semester - Work to be done: wrap up as tools for others to use, with documentation, link to Parmesh's acquisition code etc."

There was an extra meeting over a working lunch to discuss speakers for the Advances in X-ray Imaging workshop to be held on 13 June 2017; and the Fringe meeting to be held on 12 June 2017.

  • There will be 8-9 speakers on the main workshop and Jenny Woods has a list to invite - please forward alternatives etc
  • Course on savu as an introduction and advanced use - from Nicola Wadeson (MB)
  • Training session on ASTRA and invite a speaker (CR, MB)
  • Create a circular lapel badge - stateing "No FBP" (letters FBP with a red diagonal across it; c.f. to a no right turn road-sign)
  • Topics for the Fringe event: "how to do the hacking" / "how to do Not-FBP" / "joint reconstruction an segmentation" /...

Follow up meetings:

Savu Conference Call, 11 May 2017: Participants: Nicola Wadeson, Mark Basham, Daniil Kazantsev, Sri Nagella, Philip Withers, Julia Behnsen, Jakob Jørgensen

Multichannel flagship project computational resources:

  • All agree that two workstations to be acquired will be for smaller-than-production scale reconstruction, ie, proof of concept. Therefore specification not extremely critical. Also do not want too complicated setup, which might make methods developed specific to particular system, but a general, flexible setup, that other facilities may easily adopt.
  • Larger scale production: Aim to use SCARF or Emerald(?) clusters. Should have access through IMAT(?).
  • Savu uses MPI for parallelization. At Diamond each MPI process uses a separate GPU (exclusive access). GPU can be set to non-exclusive access mode, and Savu allows different processes to access same GPU. Hence many smaller GPUs not necessary (in practice having more than four in a workstation is difficult).
  • Possibly best trade-off: Two mid-range GPUs instead of one high-end. Would probably allow same or more FLOPs with same budget, and allows to experiment with multi-GPU use, relevant for massively scaling up on SCARF/Emerald clusters with many GPUs.
  • In the end, unclear whether decision was to still wait a bit for some Savu tests to happen in the next months before acquiring workstations, or given that workstations will be only for proof of concept, can proceed to acquire soon.
  • Would be good to get ISIS-IMAT datasets soon to experiment with: Winfried Kochelmann has offered access during the current commissioning time for us to acquire data sets. Timing good before fall when users start coming.

Cone-beam in Savu:

  • Currently only parallel-beam implemented. Data loading (incl metadata such as source-to-center, center-to-detector distances), internal representation, parallelization and reconstruction to be implemented. In part to be done by Savu team and by Daniil/Jakob (maybe wrapping ASTRA FDK), to be further coordinated during visit at Harwell.

Savu for laboratory micro-CT:

  • 1st step: Get Savu up and running at existing workstation with single GPU in HMXIF, try running Savu's test data sets. Awaits new version of Savu released and hopefully installation guidelines.
  • Possible 2nd step (only discussed by Julia and Jakob after meeting): Adapt for use with Zeiss Ultra nano-CT instrument data. This is parallel-beam monochromatic lab CT data. Requires importing into Savu of Zeiss data format, or of manually exported TIFF/BIN-stack plus metadata. Should be able to see benefits of using Savu functionality on this lab data with minimal effort.
  • 3rd step: Adapt for use with cone-beam micro-CT data. Can use e.g. SophiaBeads or SparseBeads (Nikon format) datasets from Zenodo to test.


  • Are Python data readers for Zeiss and Nikon cone-beam data already available in CCPi core library? If yes, are or can they be easily used from within Savu?
  • How (and when) to confirm availability to us of SCARF/Emerald clusters; how to initiate the scaling-up work?

Meeting at Working Grop and workshop: 12-13 June 2017; SN, JJ, DK, MT, EP

Presentation given:

Discussed items:

  • Workstation - single larger machine based in Manchester to be purchased; action for quotes (DK, JJ)
    • JADE (GPU cluster) login etc to be investigated MT
  • Images and ppt for flagship - uploaded
  • Datasets:
    • ISIS/IMAT; Genovere meeting to be organised DK (aim for scan time before Xmas)
      • Crab data set - XCT and Neutron tomography RG/IO
      • Kate Dobson at Durham to be contacted JJ/MT
    • Manchester hand-over for system in HMXIF - JJ to monitor and extract new test data
  • Website update - tab on main site done but needs tidying up
    • Move twiki information to drupal site (SN/MT)
  • Submission for ToScA 2017 - done
  • Leaflets/poster etc to be redone.
    • update leaflet etc (SN to send around doc)
  • Phantom: Andy King at soleil and psiche beamline. (MT to contact)
  • VR graduate student is in RAL May-August: working with SN.
  • Management meeting to be arranged for early September: then every three months.

-- MartinTurner - 24 Mar 2017

Topic attachments
I Attachment Action Size Date Who Comment
pdfpdf CCPi-core_library-a_proposal.pdf manage 35.5 K 24 Mar 2017 - 08:55 MartinTurner  
pdfpdf CCPiFlagship2017.pdf manage 1733.6 K 28 Mar 2017 - 14:03 MartinTurner  
pdfpdf CCPi_updates06_17.pdf manage 5829.6 K 13 Jun 2017 - 12:50 MartinTurner  
pdfpdf CIUK_2016.pdf manage 5761.5 K 28 Mar 2017 - 19:11 MartinTurner  
pdfpdf EP-P02226X-1proposalPartA.pdf manage 4434.5 K 28 Mar 2017 - 14:04 MartinTurner  
pdfpdf EP-P02226X-1proposalPartB.pdf manage 49.2 K 28 Mar 2017 - 14:04 MartinTurner  
pdfpdf RTMCT_kick_off_math_presentation_jakob.pdf manage 4164.5 K 28 Mar 2017 - 14:02 MartinTurner  
pdfpdf SAVU_Windows.pdf manage 54.5 K 24 Mar 2017 - 08:55 MartinTurner  
pdfpdf Spectroscopic_Tomography_in_the_Scanning_Trasnmission_Electron_Microscope.pdf manage 444.4 K 24 Mar 2017 - 08:58 MartinTurner  
pdfpdf beamhardening_march17.pdf manage 640.3 K 24 Mar 2017 - 08:53 MartinTurner  
jpgjpg descr1.jpg manage 963.4 K 28 Mar 2017 - 14:48 MartinTurner  
jpgjpg descr2.jpg manage 986.1 K 28 Mar 2017 - 14:48 MartinTurner  
Topic revision: r15 - 14 Aug 2017 - 18:44:08 - MartinTurner
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