Background

The CCP in Tomographic Imaging is progressing and since the last 6-month report, on 13 May 2014, it has built on current activities to deliver new versions of the core codes, as well as delivered benefits specified from the mid-term review findings.

The CCPi prioritises the two areas of reconstruction and quantitative analysis. It aims to provide the UK tomography community with a toolbox of algorithms that increases the quality and level of information that can be extracted by computer tomography. Key components continue to be to increase usage, training and software deposits, as well as integration of iterative methods within the toolkits.

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

Recently there is growing links with the now funded CCP PET/MR that employs similar iterative solutions for positron emission tomography (PET) solutions.

Highlights for the Current Reporting Period

Core highlights within the CCPForge software repository: - Iterative reconstruction; development has included; 1. further optimisation of the iterative code for Diamond data sets; and 2. testing of a Matlab interface by HMXIF users that has resulted in the decision to create a version with a native Windows GUI. There is currently a beta testing process undergoing at HMXIF for their XTek instrument. Next tasks are to tidy up and test the optimised Diamond version on an I13 data set with a reduced number of projections and compare to the back-projection GPU code; and extend the HMXIF interface based on user feedback, which may include support for other instruments.

Quantitative visualisation; Following on from open presentations and meetings, R. Fowler has now taken ownership of this CCPForge archive, and an initial survey of code/updates is ongoing including building, installing and testing. There are a few issues reported by the users regarding certain quantification algorithms not working on large volumes (over 10003) and from this the code base has been reorganised. A new working relationship with Loic Courtois and Peter Lee (RCaH) has started initially focussing on a new Multi Peak Thresholding routine, as well as finding further challenges from the community.

From the flagship project, progeess continues on; 1. The non-local regularization package (patch-based method) for 2D/3D tomographic reconstruction is available on GPU and CPU. The modified version of the package has been used for improving spatial-temporal resolution of the simulated and real (neutron) data; 2. Two novel methods available for multi-modal reconstruction, which can be useful for image fusion and also hybrid tomographic reconstruction, such as SPECT/CT, PET/MR etc. and 3. The work continues on embedding the set of regularization tools (CPU and GPU versions) into the CCPi iterative reconstruction code.

Outreach and networking:

1. May 21, 2014 Celebration of The University of Manchester's Queen's Anniversary Prize for New Techniques in X-ray Imaging of Materials Critical for Power, Transport and other Key Industries. The Board of Governers raised their support at the dinner following celebrations in University Place;

2. We manned a stand at the EuroVis 2014, hosted by Swansea University in the UK, that is the 16th annual visualization gathering organized by the Eurographics Working Group on Data Visualization and supported by the IEEE Visualization and Graphics Technical Committee (IEEE VGTC). 9-13 June 2014

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

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

The new series of social meetings at RAL (coffee-and-tomography) has hosted its 18th monthly meeting (total att now 266). We have also hosted the first two recorded seminars, including the Pre-Christmas talk: RAL in at RC@H: Prof Sarah Hainsworth, University of Leicester. Sarah Hainsworth will be talking on "Forensic Applications of micro-computed tomography; Bones, flies and Richard III".

Developers’ workshop occur each quarter on a new focus; 22 October at QMUL in Birmingham; informal away-day 22 July 2014 CCPi Third Developers' Workshop held at Nottingham's Hounsfield Facility; a multi-CT-machine with novel robotic-greenhouse attachment; and 20 May 2014 CCPi Second Developers' Workshop held at Birmingham.

Flagship activities: Related to the code integrated within the CCPForge, three papers have been accepted or under revision by Daniil Kazantsev;

TO DO

Widening participation: There has been through the RCaH a visiting fellow, Brian Bay, from LaVision Inc., Dr Brian Bay CCPi Fellowship Tour: @ UCL 3 July 2014 for a mini-conference (10am-5pm) then UoM and Oxford and the CCPi fellowship scheme also assisted in promoting the Drishti volume visualiser on Monday 8 September, Ajay Limaye gave a workshop and discussion of the features. (http://sf.anu.edu.au/Vizlab/drishti/) Latest Code: https://github.com/AjayLimaye/drishti after a previous show and tell at the NHM.

From the EU involvement. Two short-term scientific missions (STSMs) with iMinds-VisionLab, University of Antwerp, Belgium were funded by COST to work on improvement of spatial-temporal resolution in dynamic applications within the regularization framework of iterative reconstruction algorithms. Geert Van Eyndhoven was visiting scientist at Diamond RAL and RCaH for two weeks. D. Kazantsev will be visiting iMinds-Visionlab from 12 May till 23 May. This collaboration will potentially lead to joint publications.

CCP-ASEArch collaboration: Starting in April this work, by Evgueni Ovtchinnikov, involves numerical methods, to apply a multigrid solution to improve the issues caused by gradient based regularization coefficients in order to accelerate and stabilise convergence. This has now resulted in a publication to be submitted.

30 June 2014 TSB Kick-off meeting: A TSB project (37972-241197) with a visualisation component has been approved within the Towards Zero Prototyping programme. Titled 'In silico evaluation of manufacturing concepts for non-Newtonian products' this collaborates with Prof Rob Prosser (University of Manchester), Drs Charles Moulinec and Rob Allan (STFC/SCD), Prof Adam Kowalski (Unilever) and CDDMtec to integrate computer CFD simulation, with tomographic 3D image capture; and add the human-in-the-loop. This two year project is planned to start in September 2014.

Workshops and New Opportunities

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

1. September 2015 ToScA Symposium number 3

2. 30 June - 1 July 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 and overcome research barriers for fields such as computational fluid dynamics (CFD), computational mechanics, life sciences, and financial modelling. http://emit.manchester.ac.uk/

3. 9 March 2015 for three weeks, HPL Vulcan access for image acquisition

and; 4. links with a newly formed standards supporting panel (NPL/BSI cttee membership).

NVidia support through SCD has been offered; future opportunity to consider NVidia assistance to look at and improve code bases. This opportunity is being explored during the developer’ workshops.

Phil Trans A of the Royal Society: Theme Issue: X-ray Tomographic Reconstruction for Materials Science, has been accepted ‘X-ray tomographic reconstruction for materials science is a topic of considerable activity and growing significance in many fields of science’.

From quantitative visualisation a preference from the community for which visualisation tool system is preferred; and a possible move away from Volview to say Avizo / Paraview.

Issues and Problems

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

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

-- MartinTurner - 02 Jan 2015

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