Report from CCPi for the Period 24 June 2015 to 7 December 2015

Prof Philip Withers 7 December 2015 http://www.ccpi.ac.uk/

Background

The CCP in Tomographic Imaging has now transitioned to Phase Two with a new five-year EPSRC network funded from 1 September 2015; this has built on the previous activities to deliver new versions of the core codes as well as defined dataflow frameworks. We also have a new Drupal CMS (Content Management System) website setup to promote the coding and network activities).

The CCPi prioritises the areas of image capture including pre-processing, reconstruction and quantitative analysis as well as assisting in building frameworks connecting these areas. It's aim remains to provide the UK tomography community with a toolbox of algorithms that increases the quality and level of information that can be extracted by computer tomography. Key continues to be to increase the number of components, usage, training and software deposits, as well as the integration of new iterative methods within the toolkits.

The core team within STFC now includes Srikanth Nagella, Ron Fowler, Evgueni Ovtchinnikov and Martin Turner. Evgueni has been integrated within the group; this creates the core 1.16 FTE. Martin Turner (0.08 FTE) has the role in the secretariat position coordinating certain networking aspects of the CCP.

We had two extra funded posts, and an extra income source, with:

  1. Erica Yang had an extension (0.10 FTE) to develop further collaborations with the new IMAT tomographic beamline on the ISIS neutron spallation source.
  2. Handover for iterative reconstruction methods built by Barry Searle (about 0.125 FTE) is ongoing.
  3. 0.25 FTE has been allocated for extra IMAT/ISIS tomographic dataflow framwork integration with the Mantid system.

Formal links are formed with the recently funded CCP PET/MR that employs similar iterative solutions for positron emission tomography (PET) and magnetic resolution (MR) imaging. This has initially involved shared connection at Working Groups with a shared secretariat role.

Highlights for the Current Reporting Period

Core highlights within the CCPForge software repository:-

  1. Reconstruction Core algorithms: optimisation work of the iterative code for Diamond data sets has been handed over, with ongoing patches, and available via a ccpforge download.
  2. Quantitative visualisation algorithms: new Avizo algorithms including contributions by Erwan Plougonven are incorprted and code to correct for beam hardening code (Queen Mary/RCaH).
  3. Flagship project software outcomes: a final set of code has been being developed to compare algorithms and in CCPForge project.

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

  1. Diamond framework Savu : Nicola Wadeson is assisting Mark Basham and immediate future code will address speed including parallel performance as well as integrated ring artefact codes.
  2. ISIS IMAT framework: Srikanth Nagella's testbed is now linking for production service: http://stfc.ac.uk/SCD/research/data/44593.aspx - resaerch paper and poster have been produced.
  3. Avizo framework (University of Manchester): a complete framework is being ported within the Avizo visualisation system with interfaces for reconstruction code, segmentation and the beam-hardening sensitivity functions.

Outreach and networking:

Key outcomes:

Presence at conferences and open days include; 30 June-1 July held at University of Manchester: the EMiT (EMerging Technology) conference series brings together experts from all areas of computing to examine how to best take advantage of the changing landscape of computer hardware and overcome research barriers for fields such as computational fluid dynamics (CFD), computational mechanics, life sciences, and financial modelling. http://emit.manchester.ac.uk/ ; 8-10 July - Schools Visit and RAL Open DAys; 95 school visitor came to explore, and ~560 visitors saw various CCP presentations; and 31 October 2015 MOSI interactive day with CCPi kiosk and lego synchrotron

31 July 2015 CLF demonstration for HPL results from March Vulcan image acquisition experiments.

3-4 September 2015 ToScA Symposium number 3: held in Manchester. Major event two days of symposium and one day fo training courses.

Paper/poster at The IEEE Big Data 2015 conference recently took place at Santa Clara from Oct 29-Nov 2 - Federico Montesino Pouzols, Genoveva Burca, Winfried Kockelmann, Martin Turner, Srikanth Nagella, Derek Ross, and Erica Yang

Phil Trans Journal special issue with 11 articles was published in May specifically on CCPi activities that were based around reconstruction techniques: with a pull-up poster produced. http://rsta.royalsocietypublishing.org/content/373/2043 Theme issue ‘X-ray tomographic reconstruction for materials science’ compiled and edited by Manuchehr Soleimani

CCPi had a prime location at the Cheltenham Festival of Science in the “Dino zone”; Total public attendance was 12,100 and with schools there were 13,755 attending (plus two evening VIP sessions) over 1-7 June 2015. There were ten demonstrators created and presented (four videos and six 3D exploration models), on the CCPi touch-table, with a total of 699 active explorative viewings covering 2,052 mins (34.2 hours) of use.

Workshops / Training; We continue to support training courses within the network, from minor software license management to full training provision: four courses occurred during this period - Mantid Training Courses (16-18 February 2015) with a component of tomography vis; Diamond and ISIS CDT doctoral training working shop (9-13 March 2015) with early imaging and visualisation; (16-17 April 2015) Diamond Manchester Collaboration, CCPi and HIP, the University of Manchester and Diamond Light Source training on the visualisation and quantification of tomographic data; and a University of Manchester Avizo training session (9 June 2015).</span>

The series of social meetings at RAL (coffee-and-tomography) has now hosted its 27th monthly meeting (total attendance is at 318+(from 23rd)). The first two video recorded seminars have now been viewed 66 times.

Developer workshops occur each quarter considering a specific focus;

An extended four day Avizo framework developers meeting was held at Manchester hosted by Ali Chirazi (17-20 February 2015).

Touchscreen day at Reading University with NHM (Natural History Museum) was very useful and formed a sub-group (IVG – Interactive Visualisation Group) to promote touch screens for outreach (24 March 2015).

A Manchester Workshop focused on iterative solutions for the XTek machines (such as the released CGLS code) and planned the requirements to get them into regular usage in the labs that use these machines (28 April 2015).

Fellowships: Manuch Solemani has have some time to edit the Royal Society Phil Trans A special edition that is now published; Brian Bay, from LaVision Inc., continued his tour in the UK; the scheme will assist the Drishti volume visualiser author Ajay Limaye, visit in September 2015; two members from the University of Bordeaux, Erwan Plougonven (Dec 2014) and Dominique Bernard (February 2015), visited the UK to exchange experiences on source code integration for quantification visualisation; and Nicola Wadeson updated work for source code to make the Rapiscan RTT x-ray CT Machine usable as an experimental system (Feb-May 2015). Also Daniil Kazantsev has agreed to extend his fellowship until the end of August 2015.

EU involvement: There has been exchanges with the EU e-COST programme (EXTREME) with collaborating through workshops and conferences (links through Bill Lionheart, Mark Basham and Daniil Kazantsev). Formal meetings have occurred at the Applied Inverse Problems 2015 conference.

CCP Cross-collaborations:

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

The SLA EPSRC funded survey: the results for CCP visualisation user needs has been analysed to consider the long tail of products that the global community uses (>100 responses) and focus our CCPi core development effort on certain products. Launched on 2 February 2015: http://www.vizmatters.cs.manchester.ac.uk/index.php/Main_Page

Cross-funded links with the HIP (Harwell Imaging Partnership) have provided momentum for the visualisation facilities within the new ICAL (Interdisciplinary Centre for Ancient Life) with the Manchester Museum.

2-Day Workshop on ‘Compressive Sensing and Sparsity: Theory and Applications in Tomography’ Venue: School of Mathematics, The University of Manchester, UK, 12th & 13th November 2015. Organisers: Oliver Dorn and Martin Lotz

Industrial Projects:

The TSB (UK Innovate) project (code 37972-241197) for Towards Zero Prototyping programme. Titled 'In silico evaluation of manufacturing concepts for non-Newtonian products' is a collaborates with Prof Rob Prosser (University of Manchester), Drs Charles Moulinec and Rob Allan (STFC/SCD), Prof Adam Kowalski (Unilever) and CDDMtec aim to integrate computer CFD simulation, with tomographic 3D image capture; that will add the human-in-the-loop with EIT (Electrical Impedance Tomography).

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

23 September 2015 open day will consist of tours round North Star Imaging’s demonstration/inspection facility where you will get chance to see live demonstrations of our X5000 X-ray system. Run by NSI: http://4nsi.com/events/uk-laboratory-open-day

The third Xradia European Network Workshop is being held in Manchester on 4th-5th November

The Industrial Tomography Workshop (into2015) is a scientific conference organized at University of Antwerp, Belgium, on 4-6 November 2015. The event is part of the activities of the MPNS COST Action MP1207: Enhanced X-ray Tomographic Reconstruction: Experiment, Modeling, and Algorithms: http://astra.ua.ac.be/into2015 This included a tour of the Bruker (Skyscan) facilities (http://bruker-microct.com/home.htm).

Workshops and New Opportunities

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

September 2015 ToScA Symposium number 3 will include further CCPi activities including two fellowships for software developers' to attend (ToScA 2015 will be in Manchester and 2016 will be in Bath.) Partnership status has been applied for and advertisement including leaflets and a stand are being prepared including links with the CCP PET/MR. We will be sponsoring student travel grants.

July 8-11, 2015 Harwell Open Days including Tomography vis tools from CCPi and CCP PET/MR will be demonstrated over the days at the Atlas Visualisation Facility

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

Open session for analysis of CLF Vulcan data from recent imaging capture industrial exploitation days is planned for June/July 2015

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

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

The next "away-day" developers’ day is proposed to be at the Warwick University Manufacturing group: and future software show-and-tell events will be based on the three Frameworks.

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

A touchtable volume visualisation content discussion mini workshop is planned to coincide with the ToScA event .

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

A new data archive with community space has been setup on the zenodo website https://zenodo.org/collection/user-ccpi?ln=en This site includes test data sets from Sophia Coban; simple model scans and touchtable presentation data sets for science analysis and for public outreach and dissemination.

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

Issues and Problems

There is a still need to foster inter- and intra-networking between the developers group and the user community. We have drastically increased levels of outreach with the Interactive Visualisation subGroup (IVG) but more project and research proposals need to be submitted.

Applications for ‘good’ new Fellowships and exchange visits are difficult and needed.

Software licences are an issue including the Avizo Harwell Campus site license that expires in 2016.

The next CCPi Working Group meeting is planned to be held in June 2016.

-- MartinTurner - 01 Dec 2015

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