This is the Daresbury Science and Innovation Campus Web Server for some community building projects.

STFC Scientific Computing Department - Visual Analytics and Imaging System Group Facilities

Multi-site system to support STFC facilities especially the Hartee Centre (

People involved in this work are:

STFC Scientific Computing Department, Visual Analytics and Imaging System Group: Erica Yang (Head of the Group), Sri Nagella, Ron Fowler, Evgueni Ovtchinnikov, Emma Tattershall (6-month graduate placement, left in Mar. 2017), Martin Turner (Visiting Scientist)

STFC Hartree Centre: David Hughes (left STFC in April 2017), Rob Allan, Barry Searle, and Tom Christy.

We also work closely with members of the Virtual Engineering Centre, Lynn Dwyer and Iain Cant; and other groups across SCD. If you wish to visit or enquire about using the facilities then please email:

Links to direct facilities and those from partners:

Screens and system have been provided by Virtalis Ltd. and HARP (Visual Communication Solutions).


There are also two high-power Dell Windows and Linux workstations, with 1/2 TB RAM available for use in compute-intensive quantitative visualisation tasks; and now a Multitouch Table (1920x1080) being used as an introduction show-and-tell device.

We also have two GPU equipped Gateway Nodes installed for remote access to data from the Hartee Centre GPFS system.

YouTube videos: include

Web Description

The Visualisation Group, part of the Technology Division within SCD, has been founded to support and maintain visualisation software and skills for large projects and user communities across STFC. This includes working with the Hartee Centre hosting their visualisation centres connecting outputs from some of the largest computer in the UK making them human understandable; with the TSB Space Application Catapult and European Space Agency (ESA) producing bespoke solutions for their data analytical and command and control needs; creating remote and distance data gathering and visualisation workflows to control the computational processes and providing specialist local high-end equipment within the centres that are near to the main STFC image capturing x-ray, neutron and laser facilities.

The group is working to support the high-end visualisation centres within STFC, with the key objective to consider the human-in-the-loop as an integral part to pre- mid- and post-data visualisation needs from the major facilities, from archived data stores and from computational simulations. This it is believed is a key component to increasing the efficiency of the major STFC facilities allowing researchers' work-plans to be controlled, changed and even stopped on the fly.

The group has an emphasis to work in harmony with collaborators across the STFC mission. To this end there are links to strategic partners; as well as the Hartree Centre this includes the Virtual Engineering Centre (University of Liverpool centre based in the Daresbury Labs.), the Harwell Imaging Partnership (based in the RAL campus), the Collaborative Computational Projects (CCPs based across SCD) and a range of projects with other teams and groups within SCD and STFC.

Official STFC website with images:

Goals and Aims:

These are targets for the vis group within the forthcoming period towards 2016

  • H2020 - involvement in one or two bids
  • TSB - involvement in collaborations


Group Meeting

List of project sub-pages will appear here:

Links to HIP ( HIP wiki)

Seminars and Symposiums

These consist of:

  1. seminar sessions involving the graphics community with external speakers via the SCD Seminars
  2. data and coffee sessions on visualisation themes - topics linked through Computation Tomography;
    Next Season is planned, Atlas Visualisation Facility (RAL).
  3. other symposiums and project discussive co-hosting events.

Thirty Six Tomography Seminars have occured for the Seasons 2013-2016 (imagery is below) and details of Past and Future events available here.


semseason2014_2015.jpg sechalf2015.jpg


Please email proposals and interest:

Click here for full details of past and upcoming seminars and symposiums

Future Events and News Highlights

News Items:

September 2018, Swansea University COMPUTER GRAPHICS & VISUAL COMPUTING 2018 (CGVC2018) The 36th Annual Conference organised by the UK chapter of the Eurographics Association, UK

MMC (Microscience Microscopy Congress) 2018, 1-4 July 2018

Computing Insight UK 2017 12-13 December 2017 Manchester Central Convention Complex, Manchester, UK

5 December 2017 CCP SP Meeting at JISC, London

17 November 2017 - CCP PETMR 17th Software Meeting 12:00 to 14:00 and 6th CCP PET-MR Working Group Meeting 15:00 to 17:00

TDW/4 Technical Committee meeting, (TDW/004/04/01 Technical Product Realization XCT, committee area to be called TPR/1) 16 November 2017, at BSI in the large conference room on the ground floor (G1)

15 November 2017 CCPi Working Group meeting at ICAM, Manchester, and AVF, RAL

SCD Seminars: Raymond Chan, from the Chinese University of Hong Kong (coming on November 2nd): and Jim Nagy, from Emory University in the USA (coming December 7th): The seminars will be at 2pm on those respective days. They have been invited to participate in the Isaac Newton programme "Variational methods and effective algorithms for imaging and vision":

2017 IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS/MIC) 21-28 October 2017

12 October 2017 CCPi Exec Meeting, 3pm

11-13 October 2017 2nd International Conference on Neutron Imaging and Neutron Methods in Archaeology and Cultural Heritage (NINMACH) 2017, Budapest Neutron Centre.

9-11 October 2017, 3D Metrology Conference 2017

Visit from ThermoFisher FEI Software Group: 2 & 3 October 2017, at The Research Complex at Harwell. "Correlative & multimodal data acquisition, analysis and modelling" Contact Robert Atwood to arrange a meeting (

29 September 2017, 16:00 (BST). Diamond XCT webinar topic 'Impact of X-ray Imaging on Physical Sciences' brought to you by Diamond's Physical Sciences Director (Professor Laurent Chapon) and the Principal Beamline Scientists of I12 (Dr Michael Drakopoulos) and I14 (Dr Paul Quinn). We invite you to register for this webinar by clicking here:

The EPSRC are now carrying out a road mapping exercise: This is your chance whether you are an academic, industrialist or student to have your say about what type of facilities you would value. It is not intended to replace individual facilities across the UK but rather to provide greater opportunities for X-ray imaging than are possible in individual labs and to make sure that access is provided with a high level of technical support. It would be really appreciated if you could complete a short survey to be found at:

22 September 2017 PETMR 16th Software Framework Meeting

IMA Conference on Inverse Problems from Theory to Application; Isaac Newton Institute, Cambridge, UK 19-21 September, 2017

14-15 September 2017, Manchester Metropolitan University COMPUTER GRAPHICS & VISUAL COMPUTING 2017 (CGVC2017) The 35th Annual Conference organised by the UK chapter of the Eurographics Association, UK Two CCPi papers were presented and proceedings are online at:


University of Manchester - Lunch-and-Learn sessions in XCT (contact for details)

  • 9 August 2017 - Nghai Vo from Diamond Light Source; Martin Turner on dXCT activities
  • 13 September 2017 - Alistair Garner Advanced 3D characterisation of iodine-induced stress corrosion cracks in zirconium alloys Jose Godhino BP summer placements
  • 10 October 2017 - Adam Cooper X-ray tomographic analysis and characterization of ductile damage William Brayshaw Ductile fracture behaviour of Reactor Pressure Vessel steels
  • 7 November 2017 - Nick Curry An Investigation into Rust Layer Microstructure
  • 12 December 2017 - Sri Nagella, Diamond Light Source / SCD - STFC

Launch of CoSeC? - Computational Science Centre for Research Communities:


Research Software Engineers, the Second Conference will be held at the Museum of Science and Industry in Manchester on the 7-8 September 2017

New EPSRC RSE calls are related: see section dedicated and note State of the Nation report at:

WSSSPE5.1 is in Manchester, UK; 6 September 2017

RSE UK-USA Exchange; Marcus Hanwell from Kitware has been awarded an EPSRC grant to exchange information across related RSE groups in 3D tomographic visualisation and processing. The schedule so far is:

Many meetings and images at RAL and DL:



Presentations used the wifi barco link that is great and works - so no cables from your laptop:


Also included ws a tour of IMAT/ISIS and DLS i13




The ToScA 2017 meeting is taking place from 6-8 September at the University of Portsmouth. Farah Ahmed is Chairing the meeting, along with local Co-Chairs, Asa Barber and Gianluca Tozzi. As in 2016 the meeting begins with a day of workshops on 6 September and then the two day ToScA symposium:

Book launch from Nottingham - Springer exhibition series discuss at ToScA- pre-order from Amazon now, but the book launch will be start of October


CCPi had a stand with Touchscreen demos and HTC Vive demos running:


6-10 August 2017; 11th Developments in X-ray Tomography. Details are he re:

9 August 2017 Nghai Vo from Diamond Light Source “Developments of image processing techniques for tomographic data at synchrotron facilities" Abstract: X-ray computed tomography is a well-established technique for lab-based systems, but it is not the same for synchrotron-based systems. Many technical issues can strongly impact to the quality of the reconstructed images such as the stability of the X-ray source, the mechanical accuracy of the sample stage, the quality of the imaging system, or the capability of the computing resources. In this talk, I will show the application of various image processing techniques to deal with these issues. and Martin Turner will also provide an update on the recent dXCT conference in Warwick. Manchester Lunch-and-Learn session

"Meet A Scientist" Family Day at RAL with VR setup for ISIS beamline and tomograhy being one of nine main events; Saturaday 29 July 2017:


ISIS/IMAT Paleo Forum session with CT tomography topics: 21 July 2017


IPCC Parallel Software Workshop by The Hartree Centre 13 July 2017

13 July 2017, dXCT conference at WMG - event site exists now:


with the ccpi stand amongst a dozen others:


Including a tour of the new high-energy XCT setup:


EMiT 2017 will be held at UPV Universitat Politècnica de València in Spain between the 10th and 12th of July 2017 The final deadline for abstract submission is the 14th of April.

Release of CIL v0.x for CCPi: 30 June 2017 - see with data and docs at

3rd International Conference on Tomography of Materials and Structures, which will be held in Lund, Sweden, 26th – 30th June 2017. ICTMS 2017 is the 3rd biannual conference of IntACT (International Association of Computed Tomography), following very successful meetings in Ghent (2013) and Quebec City (2015), and will focus on the use of 3D tomographic methods for (non-medical) studies of the internal structures of materials and their evolution:

Next main CCP Steering Panel meeting will be 26 June 2017, MRC, 1 Kemble Street, London. We will organise Working Group and activities prior to this.

EPSRC Equipment Roadmap for Tomography - Initial meeting on 26 June 2017 in London, UCL; Skype conference call 21 July 1pm - email if interested to be involved:

23 June 2017; 1:30pm CCP PETMR v-streamed seminar Rigid Motion Correction for Positron Emission Tomography Brain Imaging, Matthew Spangler-Bickell, PhD, KULeuven, Belgium Abstract: A rigid motion correction technique for PET brain imaging has been developed and applied in animal and clinical studies. Results will be presented from a study on the effect of aneasthesia on the uptake of FDG in the rat brain, using fully conscious and unrestrained rats. Results from implementing the motion correction technique on four clinical PET scanners are also presented. In addition, a spatially variant resolution modelling technique which could be used in conjunction with motion correction will be presented.

CCPi Core Imaging Library pre-release teleconference to discuss about the upcoming release of the library on 21 June 2017, 25 July 2017, 12 September 2017, 12 December 2017.


including the launch of and documentation.

SCD STFC Newsletter - included some information for the Flagship CCPi grant: now has details on the main website:


15 June 2017 13.30-16.00 CCP PETMR Working Group in London and via SfB With the three Software Developer prize winners for 2017. CCP PETMR has yearly awards for the most active contributors. To qualify, you have to be an Early Career Researcher and help in any way you can (helping out on mailing lists, contributing software, participating in discussions etc). Members of STFC are excluded. The awards are decided by the CCP PETMR Executive Committee: Bronze (£100) Casper da Costa-Luis, for git magic, git and github education, and sound advice; Silver (£200) Benjamin Thomas, for the SuperBuild and CMake education and Gold (£400) Christoph Kolbitsch, for MR demos and education.


13 June 2017 "Advances in X-ray Imaging" Workshop Held in RAL and CCPi Sponsored with RCaH this will be help in DLS (G49 and atrium all reserved). Registration and speaker program:


A 'Fringe' alt meeting was on 12 June 2017 prior to this event in the Atlas Visualisation Facility.


12 June 2017 CCPi Working Group meeting 11am-2pm at RAL (Atlas Visualisation Facility)


... including cross-link with CCP PETMR.


... and a lunctime play on the VR volume viusalisation setup - demonstrated the 'mobile phone data set'


Synopsys will run a free training workshop we're running on 7 June 2017:Henry Moseley X-ray Imaging Facility, Simpleware software is widely used in academia. The workshop covers 3D image data visualisation, analysis and model generation in Simpleware software ( and includes an optional hands-on software training (

31 May 2017 - Hartree Centre new builiding opening by HRH The Duke of York KG. Included visualisation demonstrations of the VEC facilities.


PSMR 2017 29-31 May 2017 For detailed information please visit at the Olissipo Oriente Hotel - LISBOA. This event is under the auspices of the European (EANM) and Portuguese (SPMN) Associations of Nuclear Medicine. Deadline for abstract submission: 28 February 2017 There will be a PET-MRI SCHOOL on the 27th May (Saturday) for students and researchers. session on CCP sw release at 13:30-15:00

22-23 May 2017 International workshop on machine learning and data analytics in advanced metals processing work on Tomography analysis will be presented.


19 May 2017 IMAT/ISIS test tomography supported by CCPi for ICAL / Manchester Museum artifacts; with initial show-and-tell on 12 June.

12 May 2017 UCL / UCLH 3rd PET/MRI Course with CCP PETMR representation and speakers, held at the Welcome Collection


11 May 2017 CCPi Flagship developer's roundtable t-conf and face-to-face at RAL on 13 June.

11 May 2017 PETMR review meeting and preparation for software v0.9 SIRF release on 12 May 2017 - see website. This is the 14th Software Developer's Meeting and included a cmake descriptioon (open access link at


11-13 May 2017 Practical+Clinical hosted by UCL as a course for PETMR Details and registration at:

CCP PETMR presentations at The Physics Session: Thursday May 11, 2017 Objective: to stimulate discussion on specific issues that might affect cross-site harmonization.



May 2017, on the 9th and 10th, Dr Tsoumpas gave at the University of Tohoku in Sendai, Japan, to an audience of 12 students a 2 days course on PET reconstruction including practical exercises and discussing the role of the synergy between PET and MR for more accurate modelling of the acquisition process. In addition, Dr Tsoumpas presented to two seminars to attendees from PET centres in the country (Akita, Chiba, Fukushima, Tohoku) on the new developments of our network.

SuRVoS (Super-Region Volume Segmentation) Workbench is a program for segmentation of 3D image datasets. SuRVoS combines high-level algorithms for feature detection, and super-region building for smarter, quicker segmentation and analysis. A training workshop will be held at Diamond Light Source on May 4th and 5th 2017. Please bring your own data as time will be provided on the second day for individual, hands-on training. Please log on and register here:

The EGU will be held in Vienna, Austria; 23-28 April 2017. ( Please submit your abstract here: (the deadline for abstract submission for the EGU session on ‘Multi-scale 3D imaging of geological materials: new insights from new techniques’ is 11th January). Imaging work on geological materials, including the following areas, is welcome: Geochemistry, Mineralogy, Petrology & Volcanology (GMPV), Earth Magnetism & Rock Physics (EMRP), Energy, Resources and the Environment (ERE) and Stratigraphy, Sedimentology & Palaeontology (SSP) Please contact Drs Ma or Fauchille if you have any queries: or

[10 May 2017] {First data rele ase from the developing Human Connectome Project}


"the first preliminary release of data as part of the Developing Human Connectome Project (dHCP) – an ERC-funded collaboration between King’s College London, Imperial College London and Oxford University. This is the project’s first open access data release which consist of images of 40 representative term neonatal subjects. The imaging data includes structural imaging, structural connectivity data (diffusion MRI) and functional connectivity data (resting-state fMRI). This preliminary data release comes with minimal accompanying meta data: gender, age at birth and age at scan. More specific information about the available data can be found in the accompanying data release notes. To access the data visit:

You will need to register and will be required to agree to a simple data sharing agreement. We invite colleagues in the field to explore and feedback on the value and characteristics of the image dataset. The image data are processed using analysis pipelines that are subject to further development. The project to date has successfully completed 584 neonatal scans and further data is still being collected, including fetal imaging (imaging babies before birth). Future data releases will consist of comprehensive image data with accompanying clinical, neurodevelopmental and genetics information.

We hope this first data is interesting and welcome your feedback.


Contact: Professor Daniel Rueckert, Biomedical Image Analysis Group, Imperial College London, 180 Queen's Gate, London SW7 2AZ, UK, Tel: +44 20 7594 8333, E-Mail:, Web:


3-4 May 2017 Exploring Big Data and Data Science, Hartree workshop with data experts from industry and academia 4 May 2017 STFC Daresbury Laboratory, Sci-Tech Daresbury, Cheshire, WA4 4AD for: Researchers in big data analytics, data science or related fields


3-4 May 2017 SLA Staff Away Day STFC Daresbury Labs


27 April 2017 STFC/IOP joint workshop on ‘HPC for discovery at accelerator facilities’ includes a visualisation section on big-data

A Celebration of the University of Manchester's Regius Professorship of Materials: Prof Philip Withers; 25 April 2017 details at


EGU course, 25 April 2017- 3D and 4D imaging: Automation of data analysis Convener: Jose Godinho

25 April 2017, 5:30pm, NPL Manufacturer Measurement Network Innovation in Manufacturing 3M Buckley Innovation Centre Firth Street Huddersfield HD1 3BD

Avizo Training in Manchester; 18 April: Introduction to X-ray CT and Image Processing with Avizo; 19 April: Advanced segmentation and quantification using Avizo; 25 May and 13 June: Introduction to X-ray CT and Image Processing with Avizo; and 14 June: Advanced segmentation and quantification using Avizo Detail at:

30 March 2017 Tier 2 Computaing facilities EPSRC launch and information day in Birmingham:

100 Years of the Radon Transform; The conference will take place from March, 27th to March, 31st, 2017 at Johannes Kepler University of Linz. The Radon Institute of Computational and Applied Mathematics in Linz, Austria, is organizing a conference on the 100th anniversary of the publication of the famous paper “Über die Bestimmung von Funktionen durch ihre Integralwerte längs gewisser Mannigfaltigkeiten” in Berichte über die Verhandlungen der Königlich-Sächsischen Gesellschaft der Wissenschaften zu Leipzig. Mathematisch-Physische Klasse, Band 69, 1917, Seiten 262–277, of the name giver of the institute, Johann Radon.

20 March 2017 pre-Flagship meeting at RAL: Meeting Room 1: RCaH: Lunch at i13 Meeting Room: all welcome 2-3pm Project planning meeting; 3-4pm Open session and short presentations



MRI touchscreen datasets and images on display at British Science Week 13 March 2017

Two new flagships approved:

9 March 2017; 12:30 to 16:00 The 13th CCP PET-MR software meeting at the University of Leeds afterwards at 16:00-17:00 a Flagship steering meeting


XCT user meeting Wednesday, 8 March 2017


TMS2017 (San Diego) Session on Defects and Properties of Cast Metals TMS2017 Annual Meeting in San Diego - there will be several sessions on solidification and casting. We hope that you will submit an abstract to the symposia on ‘Defects and Properties of Cast Metals’, and ‘Applications of Solidification Fundamentals’. For more details see the TMS website: Sunday, 26 February, 2017 to Thursday, 2 March, 2017

iCT 2017: the 7th Conference on Industrial Computed Tomography being held in Leuven Belgium between the 7th and 9th of February 2017

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' Held at RAL and via Video Conference. See for physical and video stream link access.


Jigsaw24 virtual reality event at their Golden Square centre on 8 February 2017, from 5pm-10pm

Monthly TechVis session 2pm-3pm on the first Monday of each month (6 Feb, 6 Mar, 3 Apr, 1 May, 5 Jun, 3 Jul, 7 Aug, 4 Sep, 2 Oct, 6 Nov, 4 Dec 2017) held at RAL Atlas Visualisation Facility and distributed by BlueJeans link (see for links:

"dragonfly" webinar (3 February 2017) was broadcast on their quantitative vis tools - we have some contact for academic licenses please email. Recording available at:


31 January 2017 Software Show-and-Tell 2pm in the RAL Atlas Visualisation Facility: Mark Baham 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: live streaming to the PSI Seminar Room (3.306, Alan Turing building) in the University of Manchester.


Avizo Introduction course, 26 January 2017: please email; 9.30-16.30 University of Manchester 3.306 at PSI (Alan Turing Building) Course fee: £500 is applicable to all external users who are not students / members of staff at the University of Manchester.

SCD Newsletter article for vis and lego


26 January 2017 Applied Visualisation Community Forum, taking place at the British Motor Museum, Gaydon, Warwickshire. Please register for the event at:

16-17 January 2017 5th UK & Ireland FOAM/OpenFOAM User Day. Venue: School of Mechanical and Materials Engineering, University College Dublin: Details, including registration (the event is free), can be found at the website:

16 January 2017 CCP PETMR developers session - ICAM room in Manchester please book at: Lunch available from 12:30pm - meeting from 1pm


11 January 2017 BSI standards meeting of the XCT panel (TDW/4/4/1) 10.30am at BSI in West London

RSE Software management workshops: 9-25 January 2017: To register for one of the workshops, follow this link: (University of Birmingham, 9 January - London, the British Library, 12 January - University of Cambridge, 16 January - University of Leicester, 19 January - Engine Shed, Bristol Temple Meads, 20 January - University of Sheffield, 25 January)

9-12 January 2017 Workshop in Switzerland focused on the visualisation of complex imaging: Some of the main topics: 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.


A new EU COST proposal has been submitted - link to past EXTRMA is available (Evaluation Feedback Monday, June 19, 2017 @ 17:00)

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14-15 December 2016 Computing Insight UK 2016 over 250 delegates and suppliers present - and some tweets on the vis presentation (so far)

ciuk2016visw.jpg ciuk2016visw2.jpg

13 December 2016 Analytic Visualisation Features: show-and-tell Afternoon session hosted at Atlas Visualisation Facility. Topics include:- Reading Diamond nexus data into Avizo, paraview and ImageJ. · Loading nexus data from Avizo scripts · Using python in Avizo. · Running CCPi quantification algorithms. Please suggest any other topics and your data problems: contact Sri,

Thursday 8 December 2016, at 3pm in Frank Adams 2, University of Manchester. Speaker: Prof. Raphael Hauser from the University of Oxford. X-ray Tomosynthesis with Nonlinear Compressed Sensing Raphael Hauser, Oxford Mathematical Institute Joint work with Maria Klodt, Oxford Mathematical Institute Abstract: A new generation of low cost 3D X-ray tomosynthesis systems is based on multiple X-ray sources distributed on an emittor panel. When photons emitted from two or more sources have spatio-temporal overlap on the detector panel, partially convolved measurements ensue. We will discuss nonlinear compressed sensing models and algorithms to deconvolve the measurements, resulting in 3D image reconstruction.

IMARIS demonstration at Manchester 6 December 2016 (company visit postponed)

Avizo courses will be running at Manchester on 6&7 December 2016. If you are interested, would you please email ( with your name, the name of organisation (School/ Faculty, University etc.) and course title(s) you wish to undertake. Courses 1: Avizo Introduction (20 places) and 2: Advanced Avizo (10 places)

5 December 2016 CCP Steering Panel at London in MRC

Annual Scientific and Networking Meeting: Up and Coming Techniques in Medical Physics Translated into Clinical Practice 2 December 2016 10.30 – 17:00 (registration & coffee from 10 am) Institute of Physics, 80 Portland Place, London, W1B 1NT

Innovate UK Mixer project: 11am-2pm, 1 December 2016 in Manchester

Twelce software release meetings for PETMR: "First Release Candidate Prep meeting 1 to 8" Friday 10:30am - 25/11, 2/12, 9/12, 16/12 then in 2017 Friday 2pm 6/1, 13/1, 20/1, 27/1 - Links for joining;

24 November 2016 FEI visit and Workshop on Avizo at RAL: Developers will be available for consultation - time to be decided nearer the time. See Sri Nagella for details. (att 12+1)

Workshop in the afternoon of Wednesday 23 November 2016 at Imperial with the aim of engaging the UK materials modelling community with the activities of the Sir Henry Royce Institute (att 57).

NPL event - 1st 3D Metrology Conference: 22-24 November 2016 in Aachen 'dedicated to the application and development of 3D measurement' Some interesting agenda topics.

21 November 2016 CCPi Working Group Meeting: agenda items at:


Radiotherapy+'s New website is available and is launching funds for sandpits and PhD scholorships:

New Shared data repository on dropbox - without DOIs etc - are at: Includes the mobile phone data set in different resolutions etc.

14-18 November 2016 Supercomputing 2016 including a subitted video (to the extended showcase) with ULTRA and partners in IMAT. Teaser image:


Videos and interactive volume visualisation system (seen on top left in tweet image below) is at stand #1137:


14 November 2016 CCP PETMR Working Group Meeting 13:30 to 15:30 with improved architecture structure to also be discussed at 11th Software Metting 15:45-17:15. Both meetings will be held in London (Institute of Education - Bedford Way (20) - 417 - Committee Room 1 Agenda items:



9 November 2016 4-6pm University of Manchester, School-University Partnership Initiative (SUPI) with touchscreen showing various volume visualisation objects

9 November 2016 Seminar: Dual-tracer 18F-FDG:18F-NaF PET/MR for quantitative multi-parametric cardiovascular imaging Speaker: Dr. Nicolas A Karakatsanis from the Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, New York. PET imaging seminar that will take place at the University of Leeds (Seminar Room 8.34b, Worsley Building, Clarendon Way, LS2 9NL) at 12-1pm.

7 November 2016 CCPi CoIs and Developers' Meeting

3 November 2016: 2016 STIR Users' & Developers’ Meeting is available: This year the event will take place on Thursday, 3 November, 19:00-21:00 in Strasbourg (France) during the IEEE NSS-MIC ( - Room Varsovie, Palais de la Musique et des Congrès. Please, register your interest in attending:

IEEE MIC 29 October - 6 November 2016

New ACER laptop installation and engagement role: at MOSI and SC'16


RCaH's Royal Society exhibit travels to Manchester Science Festival for satellite exhibition on 24-28 October 2016

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EPSRC software review session - 10am-5pm on 24th October 2016 in London

19 October 2016 Lunch and Learn review at Manchester on ToScA


as well as a SCD Newsletter article on visualisation team at ToScA 2016


Avizo Intro Course - interested please email; with your name and name of organisation: 13th October, Thursday 9.30-16.30 Venue: 3.306 at PSI (Alan Turing Building) Course fee : £500 applicable to all external users who are not students / members of staff at the University of Manchester.

10 October 2016 IMAT launch event at Harwell Campus (RAL): links with a poster from SCD /CCPi. Organised at ISIS by Philip King.


Visiting CCPi Fellow; Friday 7 October 2016 Seminar 1pm in University of Manchester, Williamson building, School of Earth and Environmental Sciences, room G03. "Advanced 3D and 4D X-ray imaging techniques for the morphological and textural analysis of geomaterials" Lucia Mancini1 Elettra-Sincrotrone Trieste S.C.p.A., 34149 Basovizza (Trieste), Italy beamline scientists of the SYRMEP beamline at the Elettra synchrotron light source. Dropbox Link to recording is available.

6 October 2016 STFC Graduate Induction Day at DL: including four visualisation taster sessions using a mixture of TomViz and Drishti-Prayog on the large 3D wall.

PETMR Exec update meeting 5 October 2016: Skype for Business session

SCD Highlights document has a visualisation section for work done with the IMAT (ISIS) integration:


21 September 2016: 10th PETMR Software Meeting, UCL, morning (10.00-12.00) combined with UCL PET/MR Symposium 21-23 September 2016

New CCPi Leaflet is available, the Autumn 2016 issue:


... and new leaflets from Manchester; collection of eight 'Inside' cards


15-16 September EGUK CGVC - short paper on an EPSRC SLA survey result for CCPs that was presented held in Sunny Bournemouth - even had a hotel seaview (just - left image):


13-14 September 2016 Data Days at RAL - including a soft-lauch of the Ada Lovelace Centre and Workshop on Large Data (inc facilities) for future STFC workflows.


12 September 2016; 4pm-5pm Novitom, are visiting RAL on beamline optimisation and 3D capture - host is 3Dmagination (Loic Courtois)


RSE symposiums including: 4th Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4) 12-14 September 2016

Advanced Summer School MART-3D will take place at Carcans-Maubuisson (on the Atlantic Coast near Bordeaux) from the 12th to the 16th of September 2016. Comprising 20h of lectures, 6h of demos and plenty of time for informal discussions. MART-3D is sponsored by the CNRS, the Bordeaux University Labex Amadeus, and by the Cost Action EXTREMA. Pre-registration

8 September 2016; 3pm-4pm at RAL AND 12 September 2016 3pm-4pm at University of Manchester - Visit by Marcus Hanwell (Kitware Inc) for product show and tell

Workshop on PET-MRI Image Reconstruction on the 7 September 2016 ( ) ... part of the annual scientific meeting of the British Chapter of the ISMRM in Leeds (7-9 September). Register for the workshop via the main meeting website: (22 Meeting of the British Chapter)and encourage to submit (by Thursday 23 June) an abstract to the main meeting.

Sep 7: PETMR informal gathering for those attending ISMRM-BC, Leeds, proposed 11.00-12.00. combined with PET/MR educational workshop and the 22nd Annual Scientific Meeting of the British Chapter of the ISMRM in Leeds (images from Harry Tsoumpas).


ToScA 5-7 of September 2016, held at the University of Bath. We had two stands:



And many events during the three days. CCPi posters include:

...and Bill Lionheart et al.'s talk

Rich and Nonabelian Tomography: strain and magnetic fields; Lionheart,William; Desai,Naeem ; Schmidt, Søren; Withers, Philip




Pre-ToScA Workshops on Monday 5th September 2016 at the University of Bath in Building 4 East, level 2, room 32.a covered Avizo, VGStudio Max and Drishti. [FEI Pore network modelling using Avizo (9:00-11:30); VGStudio MAX 3.0 (12:00-2:30); Drishti/Prayog (3:00-5:30)] Part of the symposium so much discussion after the training over good food and drink.


CINEMAX Summer school (August 29 – September 2, 2016) is a five-day summer school for Master and PhD students on '3D modelling and Imaging of Material Microstructure' Denmark:

Launch of ICAL site and listserv accout: for partners within Manchester Museum Request "... email the list when they publish a paper pertinent to ancient life - that way we can all know what other people are up to, and also then I can add it to the ICAL website publication list, and create an item in the news section."


28 August - 1 September 2016 SPIE Developments in X-Ray Tomography X:

15-19 August 2016; X-ray Microscopy 2016:

A series of Avizo courses will be running from 16 to 18 August 2016. in Manchester- Course fees are applicable to all external users. 1. Avizo Introduction (20 places) 16th August, Tuesday 9.30-16.30; 2. Avizo Advanced (10 places) {Advanced segmentation (AM), Quantification (PM)} 17th August, Wednesday 9.30-16.30; 3. High-resolution Imaging (8 places) 18th August, Thursday 9.30-16.30


12 August 2016 RAL show-and-tell; TIGRE cone beam CT software in GPU: Ander Biguri and Manuch Soleimani, University of Bath: RAL AVF (Atlas Visualisation Facility) and VC to Whitworth Room in DL - local host Sri Nagella.


Showed new video conferencing utility in action.

11 August 2016 RAL CCPi Interactive Vis - Show-and-Tell : RAL AVF (Atlas Visualisation Facility) and VC to Whitworth Room in DL - local host Sri Nagella.


From the vis meeting in UCL a view of your parter Radiotherapy Network+ new hole in the ground for their accelerator installation.


For our next INM seminar, we are delighted to host a talk by Prof Rich Carson (Yale PET centre): Title: Tracer Kinetic Modeling in PET: Model development and direct reconstruction Time: Wed 3rd August @ 17:00 Location: Chadwick B05 LT, UCL Abstract: When PET imaging is combined with tracer kinetic modeling, quantitative measures of receptors, transporters, and enzymes can be obtained on a regional or voxel level. This presentation will provide examples of the development of appropriate models for novel radiopharmaceuticals including the production of parametric images of these physiological values. First, a summary of the development of models for a kappa opioid receptor antagonist will be presented. Next, nonhuman primate work will be shown allowing the quantification of Bmax and Kd for a glycine transporter ligand. Finally, methods for direct reconstruction of kinetic parameters (where the kinetic model is incorporated into the list-mode reconstruction), including dynamic scatter and motion correction will be presented.

Aug 3: 9th PETMR Software Meeting, UCL, 13.30-16.00 (lunch from 13.00) combined with talk by prof. Rich Carson (Yale PET Center) at UCL 17.00 and before an Exec Meeting.


SSI Vis day on 28 July 2016

ESOF event at Manchester - CCPi stand at the Great Hall in the Sackville Street Building

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There were also Rift example - an image from Astronomy, University of Manchester


Hartree Centre Courses: wc 13/June Big Data - 27/June Engineering Simulation - 11/July Visualisation - 18/July HPC

14 July 2016, 11:00am at DL SCD Seminar, Hamish Carr (University of Leeds), "Topological Analysis and Visualisation"

12 July 2016 CCPi Core Developers Meeting: Video Conferencing ICAM and RAL (and link to University of Bath)

1st ESMI Imaging Technology Summer Workshop TOPIM TECH on “MULTISCALE and MULTIPARAMETRIC IMAGING”; 10-15 July in Chania, Island of Crete. R egistration and further information visit

Present your work at the 3rd International Congress on 3D Materials Science (3DMS 2016). Fast forward your materials research impact by presenting at 3DMS 2016, where you will have the chance to connect with your colleagues in the 3D materials science community July 10–13, 2016 St. Charles, Illinois

24th Summer School on Image Processing from 7th July to 16th 2016 at Szeged. This year we have sponsorship from EU COST Action MP1207 to reimburse 4 students from EXTREMA countries. Moreover students from central European countries are able to apply for freemover CEEPUS grants to cover their participation costs ( Details at:

Crocodile issues: images and studies from Manchester Museum and STFC - credit for data sets goes to Alan Brown from STFC and Campbell Price from Manchester Museum, Curator of Egypt and Sudan. Created below is an animated GIF of a scaled down version from the 8K hi-res image used on the main vis wall at the Hartree Centre but it still shows some of the exploration available:


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”. They’ll be looking inside materials from ice cream to volcanoes to batteries to see how the internal structure of materials changes as you process it or just use it in service. They’ll have models of a synchrotron, a lego tomography beamline, and lots of results off of the I12 and I13 beamlines. All are welcome to visit, see details at: Photos from others at the event:


Open Days included a continual CCPi presence with passive visualisation:


and the MS touchtable:


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.

Corporate day


Schools day


Public day



6 July 2016, 2pm SCD Seminar: Dave Pugmire (Oak Ridge National Laboratory), "In Situ Visualization and Analysis Services for Extreme Scale Supercomputers" repeated on 12 July 2016 at DL.

1 July 2016 Data trandfer test with GlobusFTP? from DLS to Manchester - there are fast parts but end point completed and took 206GB in 3 hrs.

KCL course for PETMR 29-31 June 2016 Simultaneous PET-MR: Technology and Applications

Hartree Summer School - showed Image Based Modelling examples were shown and described: 28 June 2016


CCP Steering Panel meeting is 24 June 2016 at Bristol University. Chair of the Steering Panel, Adrian Mulholland.

Fun event was Manchester Brain Box data showing the touchcreens persentations - "Two" at once smile 19 June 2016 This showed XCT / MRI and PET images for brains from flies to us; all interactively sliced and segmented. Total through the Town Hall was in excess of 5400: 90 people crawled through the 'pretend' MRI scanner and received a scanned image of 'their' brain.


13 June 2016 Drishti workshop (9:30 start in the visualisation suite in HMXIF at Manchester, 12 places). Practical workshop so attendees will cover how to convert tomography data into Drishti format, process and export it to the interactive software for display on a touchscreen. Images ready for Brainbox:


TOPIM TECH Workshop on MULTISCALE and MULTIPARAMETRIC Imaging 10 - 15 June 2016

Workshop @RAL on Advances in X-ray Imaging: Expanding the Frontiers of Knowledge 10 June 2016 Over the past decade, X-ray tomography has made significant progress with respect to spatial, temporal resolution and imaging modality. Presentations will illustrate current achievements and future developments in techniques such as computed laminography, refraction tomography, in-line phase contrast tomography and X-ray colour imaging. - Thilo Morgenmeyer “Synchrotron laminography applied to mechanics of materials”, Mines ParisTech, France; Fabien Leonard “Synchrotron Refraction Tomography”, BAM Berlin; Simon Jacques “Recent advances in X-ray based chemical imaging”, UoM/UK Catalysis Hub; Nikolay Osipov & Stephane Quilici, Mines ParisTech, France: Zset: non-linear material & structure analysis ; Peter Lee “4D imaging of dynamic processes”; Michel Bornert “In situ testing and XR-µCT imaging for the investigation of deformation and damage mechanisms in civil engineering materials.” Ecole des Ponts ParisTech, France; Gianluca Tozzi “Application of Digital Volume Correlation for the experimental investigation of bone tissue and biomaterials”, University of Portsmouth Registration site is:



Our "Fringe Meeting": was on the day before.


9 June 2016 Collaborative Future X-Ray Roundtable. Prior to the Workshop on 10 June - there wil be a opportunity to discuss with the speakers potential collborations; Cutrrent list:- Simon Jacques “Recent advances in X-ray based chemical imaging”, Nikolay Osipov and Stephane Quilici"Zset: non-linear material & structure analysis", Thilo Morgeneyer “Synchrotron laminography applied to mechanics of materials”. This will be available via video conferencing. Eventbrite site to be launched soon - contact

8 June 2016 - Developers mini-day in Southampton. New CCPForge repository set up.


7-10 June 2016, Coherence 2016:

CCP PET_MR WG 6 June 2016 in London. Register at:


The 8th PET-MR Software Framework meeting will be held on Monday the 6th June from 10:30am to 12:30pm. The event will be held in the same location as the CCP PET-MR working group meeting scheduled for the afternoon of the 6th June. A joint buffet lunch will be provided from 12:45.


EMiT2016 co-hosting event with the Mont-Blanc project ( at the Barcelona Supercomputing Centre in Spain; two day event between 2-3 June 2016, website at:

Poster presented at PSMR 2016 May 23rd – 25th 2016 Maritim Hotel Cologne / Germany


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).

17 May 2016 CCPi Core Developers Meeting: Video Conferencing ICAM (Manchester) and RAL, 4pm

17 May 2016 CCPi Working Group Meeting 12noon-4:30pm: Video Conferencing Manchester (ICAM) and RAL (S44 room in R89)


17 May CCPi Seminar planned at 11am-12noon in RAL

10 May 2016 (Tuesday) XCT Conference. May 2016 Dimensional X-ray Computed Tomography Conference 2016 Venue: National Physical Laboratory Teddington UK: I nfo: NPL web link: XCT conference-2016

Visualisation Away Day at the AVF (RAL)


Included an impromptu presentation by visiting lecturer Dr Hamish Carr:


Network Launch Town Hall meetings - Advanced Radiotherapy - 22nd April at Imperial 27th April at the Cockcroft Institute.


The Fourth UK & Eire OpenFOAM User Day University of Exeter, Harrison Building, North Park Road,-3.535704,16z Monday 18th and Tuesday 19th April 2016. Start with a beginners' tutorial at 9:30am on the Monday morning, followed by intermediate tutorials after lunch. On the Tuesday morning, there will be presentations, followed by a group discussion after lunch.

Software Developers' meeting: 22 April, Manchester, CCP PET-MR.


7 April 2016 Drupal CMS Course for all CCPs at Daresbury labs. Also a data transfer test from DLS to UoM: "It took 4hrs to transfer 210GB data at nearly 14.5MB/s".


Mantid Training Courses April 2016 at ISIS, RAL: (interested in any other these courses please send an email to Wednesday 6th April 1-5pm: Mantid Introduction "An introduction to the Mantid interface, how to graph and visualize your data, manipulate it with the built in algorithms, together with an introduction to curve fitting and live data analysis." Thursday 7th April 9-12am: Introduction to Python "This half day course will introduce you to the Python scripting language, no previous experience required, although some understanding of loops and conditional (if .. then) logic will be expected." Thursday 7th September 1-5pm: Python in Mantid "This course concentrates on using Python to build analysis scripts within Mantid as well as controlling the Mantid GUI from python, and accessing the underlying data within Mantid workspaces." F riday 8th September 9-5pm: Extending Mantid using Python "For the more adventurous among you this full day course will introduce you to the many ways you can use Python to extend the capabilities within Mantid adding Python Algorithms and curve fitting functions, as well as diving deeper into the structure of workspaces."

April 4-6 2016: Training School on Algebraic Reconstruction Methods in Tomography: and then April 6-8: HD-Tomo Days: In the training school we give a rigorous mathematical description of the reconstruction methods, the associated algebraic models, and the underlying linear algebra, followed by hands-on MATLAB computer exercises that illustrate these methods. The goal is that the participants will get a basic understanding of the formulation, implementation, and use of the algebraic methods, and thus be able to use them for their own CT problems. The workshop aims at bringing together researchers who are interested in mathematical and computational aspects of modern tomographic imaging methods that build on advanced PDE analysis, regularization, and optimization. It will feature invited talks, contributed talks, poster presentations, and dedicated discussion sessions. The goal is to demonstrate the latest tomography-relevant research by leading experts, to allow young researchers a chance to present their work, and to provide a forum for direct exchange of knowledge, perspectives, and ideas.

EU COST MP1207 Event: Combined Training School ASTRA toolbox and PhD school on Mathematics of Tomography in Copenhagen 4-6 Apr 2016

MXIF - Avizo Adavanced course, 30 March 2016, Advanced segmentation and Advanced quantification. If interested please email with your name and name of organisation. 9.30-16.30 Visualisation Area at HMXIF (Room 3.309 Alan Turing Building) Course fee : £500 plus VAT This fee is applicable to all external users who are not students / members of staff at the University of Manchester.

Simpleware webinar "Simpleware 3D Image-based Solutions for Materials Science" on CFD in tomography etc - Wednesday 23 March: recording available from the Simpleware Forum:,24.0.html


The Software Sustainability Institute’s annual Collaborations Workshop 2016 (CW16) + Hackday focusses on hot topics, sharing of best pratice and nascent tools and approaches in research software. CW16 takes place from 21-23 March 2016 at the Royal College of Surgeons of Edinburgh, Edinburgh, UK.

21 March 2016 CCPi Core Developers Meeting: Video Conferencing ICAM (Manchester) and RAL, 4pm

New networks:

  • CA COST Action CA15209 European Network on NMR Relaxometry
  • News article on advanced radiotherapy network

20 March - ICAL Machine - tagged and used for Manchester Museuem collaborations


16 March 2016, Lunch Seminar, Michael McCarthy (NPL), University of Manchester HMXIF, "Industrial XCT: Current develops of a dimensional verification standard for XCT (ISO 10360)”


CCP SLA Impact Workshop - two half-day event at Daresbury Labs. 10-11 March 2016:


CCP PET-MR Software Framework meeting will be Friday 13.30-16:30 on the 4 March 2016 at St Thomas, KCL, London. Eventbrite link with info:


University of Manchester Image-based Modelling Club Seminar: "3D Image Visualization, Analysis and Model Generation with Simpleware" Dr Celia Butler 1200-1300, Wednesday 24 February 2016 G37 Sackville Street Building, University of Manchester "This technical seminar is aimed at those interested in visualizing, measuring, and meshing 3D image data to generate 3D Printing, CAD, and Finite Element models. We will demonstrate the ease of obtaining high fidelity meshes from 3D image data, discuss new features of the latest version, and will show the workflow of processing and meshing image data for a variety of applications such as Aerospace, Oil & Gas, Consumer Products, Automotive, and Medical Devices." Further details and registration are provided at the following link:

Avizo Course Tuesday, 23rd February. 20 places (contact with your name and name of organisation): 9.30-16.30 in 3.306 at PSI (Alan Turing Building) for morning session Course fee : £500 plus VAT all external users who are not students / members of staff at the University of Manchester.

Website relaunches with Drupal CMS:-



Leeds medical imaging seminar Wednesday February 10th in Room 8.49N Worsley Building, Leeds at 4pm. Professor Terry Jones, Visiting Professor at the University of California Davis, will present his talk on: "Improving the Sensitivity of Positron Emission Tomography" Abstract: Positron emission tomography (PET) is the most specific and sensitive means for imaging molecular pathways and interactions in humans. However, the axial field of view (FOV), and hence the axial length of the body, which current PET scanners can image at one time is less than ~25cm. This limited FOV means that less than 1% of photons emitted by the radiotracer in a human subject are actually detected. To realise the full sensitivity of PET for imaging humans a 200cms long scanner is required. To this end, a recently funded USA National Institutes of Health program to build the world’s first total-body PET scanner will be described together with the expected step changes this technology will bring in the applications of PET in clinical research and health care. Contact Harry Tsoumpas

9 February 2016 CFD Unilever-Hartree update meeting Q4 start (+5months) after project restart held at Manchester

CCPi Core Developer review session, 4pm at University of Manchester; Monday 8 February 2016

SCD SLA Steering Committee panel meeting 4 February 2016. ... a follow on from this, is a EPSRC SLA workshop that is planned for 10-11 March 2016


EU COST MP1207 Event: Workshop on Big Data and Big Computation for Tomography in Szeged 25-27 Jan 2016

PET-MR developers day 2:30pm-5:00pm January 18 2016 - emphasis on MR reconstructioon API development. Room booked in London.

BSI Workshop on proposed XCT standards Thursday, January 14, 2016

Tomo-and-Coffee 2:00pm-3:00pm Wednesday 13 January 2016 Jakob Sauer Jørgensen "Limited-data X-ray tomography and sparsity regularization" at RAL Included tours and later experiments.


January 2016 issue of SCD Newsleeter included erview of the main ToScA 2016


EU COST MP1207 Event: Lorenz Workshop on Quantitative tools for Tomography in Leiden 11-15 Jan 2016


17 December 2015: Dr Biao Cai (Research Complex at Harwell) "Alloy solidification under external fields via time-resolved synchrotron tomographic quantification" MXIF, University of Manchester, Room 3.306 Abstract: Applying external fields/forces, including magnetic field, mechanical deformation and thermal gradient, to solidification processes can manipulate solidifying microstructures of alloys, which promises to significantly improve the properties of finial engineering components. The recent advancements of high speed synchrotron X-ray tomography provide a unique opportunity to obtain further understanding into how solidifying alloys respond to external fields in a quantitative manner. The talk will highlight our recent work on the usage of high speed X-ray tomography, combined with bespoke in situ rigs (the thermo-mechanical rig P2R and, and the temperature gradient furnace MagDS), to investigate alloy solidification under various external fields, focusing on the application of deformation. Advanced tomographic quantification methods applied to those time-resolved 4D datasets, including digital volume correlation and image-based modelling, allow us to resolve the microstructure development in detail, revealing key mechanisms determining the responses of semi-solid microstructures when external fields are imposed.

CCP SP Monday 14 December 2015: 11am-3:30pm Including CCP related tour of ISIS:


“’Bring/Discuss-Your-Own-DataSets’ and see Virtual Reality visualisation” held at the RAL Atlas Visualisation Facility Tomography-and-Coffee 1500-1630, 14 December 2015 RAL (Harwell Campus). "This session will also announce the launch of the new CCPi website ( Tomographic Imaging). With new license services being negotiated we are looking again at the Avizo VR toolkit: this provides an opportunity to explore your data interactively in 3D. Contact to discuss data transfer prior to the event or just turn up to see and discuss. This time there will be no video conferencing but we are happy to make this a roadshow to your location.

10 December 2015 CCPi visit to WMG: Developers Day Please Register at: Warwick Manufacturing Group , Coventry , United Kingdom.


Computing Insight UK 2015 Computing Insight UK will take place on the 8-9 December at the Ricoh Arena, Coventry – replacing the renowned Machine Evaluation Workshop (MEW). The event builds on the heritage of the MEW and offers the chance to hear about the latest developments in high performance computing, cloud and data analytics.

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A series of Avizo courses will be running from 8th to 15th December at Manchester. If you are interested, would you please email 8 Dec - X-ray CT theory (AM), Avizo Introduction (PM); 10 Dec - Advanced segmentation (AM), Quantification (PM); 15 Dec - Reconstruction

CCP PET-MR Working Group, Monday 7th of December @ UCL, 13.30-15.30. Remote attendance via webex will be possible . Location: UCL, Rockefeller Building Room 339, 21 University Street, London, WC1E 6DE Sandwich lunch will be available from 13.00.


Release of V1.0 SCD Effiecient Report 2 December 2015 - highlighted CCPi's potential for saving energy by cenrtalising compute and allowing remote visualisation. "This sharing extends to new developments; SCARF and other SCD resources are being made available for analysis of data from the new IMAT instrument. By making SCD compute resources available, ISIS does not need to invest in new high-end servers and the man-power to support them. Further, ISIS can also take advantage of software developed in SCD (CCPi) and Diamond on the common platform; this in turn can be made available to DLS users within the common platform."

Thursday 26 November 2015 CCPi Working Group meeting in RAL/Harwell Campus at the Atlas Visualisation Facility.


SCD Seminar on Interactive displays 26 November 2015; 10:30am in Atlas Visualisation Facility.


Clint Davies-Taylor (SIMULIA) giving a seminar in which he will update staff and students regarding the suite of simulation tools now available through Abaqus. Abstract " ... SIMULIA - The Power of the Portfolio. This is a one-hour presentation in which I will introduce the Corporation, Brand and Powerful Suite of products that make up the software portfolio of SIMULIA packages namely Abaqus, Tosca, Isight and fe-safe, that you now have at The University of Manchester. Then I will show some industry examples of what it is possible to do with our software and take questions." The meeting will be held from 1100-1200 on Wednesday 25 November in Room 6.207, University Place; University of Manchester.

CCP PET-MR Developers Day - University of Leeds and on webex (16 total), 20 November 2015


New CCPi and CCP PET-MR websites go live 19 November 2015

Upcoming 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 Workshop Description: Compressive sensing and sparsity have experienced intensive attention and research interest during the last 10 years in a large variety of applications, including imaging and tomography. The idea is to make use of the fact that many images or signals are sparse in specific problem-dependent bases or frames. Exploiting sparsity is usually a hard combinatorial problem. A breakthrough has been obtained when it was shown that, under certain conditions (usually including linearity of the underlying problem), the output of an l1 minimization routine or other convex and non-convex optimization methods can produce sparse results. This has opened a wide area of research ranging from theory to numerical schemes and further to applications. When it comes to nonlinear problems, the goal to obtain sparse reconstructions is by far less understood. This workshop is aiming at connecting latest results on compressive sensing and sparsity in linear tomography problems to the quite novel area of sparse reconstructions in nonlinear inverse problems. Participants are selected from a more mathematical background (theory and algorithms) towards engineering scientists working on practical reconstruction problems. Thereby this workshop is highly interdisciplinary (and also intra-disciplinary).

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: This included a tour of the Bruker (Skyscan) facilities (



The 2015 STIR Users' & Developers’ Meeting: Thursday, 5 November, 18:30-20:30. Please, register your interest in attending: Free dinner boxes will be available from 18.15 to those who come first.

.... also a workshop on Open Source Software in Medical Imaging Saturday, 7 November, 13:00-16:30 Both events are kindly sponsored by GE Research and the Collaborative Computational Platform for Synergistic PET-MR Reconstruction

The third Xradia European Network Workshop is being held in Manchester on 4th-5th November (Barnes Wallis Building). Deadline for registration is 15th October. The conference is to keep yourself updated on the latest technologies/techniques under development by Xradia/Zeiss. Manchester is signed up to the Xradia European Network as an Institution so the conference will be free of charge. Please register using the link below.

4 November 2015 9:30am: RAL/Harwell Campus and Henry Mosley XIF, Manchester; test data storage and transfer experiment; testing speed and network bottlenecks, disk read write speeds, authentication. Other parties welcome to join future phases of test.

FEI are visiting RAL us on 3rd of November and giving a short tutorial on Avizo (coordinator start at 9:30am in the AVF at RAL

Avizo course, Tuesday 3rd November: 20 places (email with your name and name of organisation. 3rd November, Tuesday 9.30-16.30 Morning session will be held at 3.306 at PSI (Alan Turing Building) Afternoon session will be taken place at Visualisation Area at HMXIF. There is now a course fee : £500 plus VAT for external users who are not students / members of staff at the University of Manchester.

The 3rd UK and Ireland OpenFOAM Ext user day(s) will be held at Daresbury Laboratory in Warrington from the 2nd until the 4th of November. Registrations are open at the following web address:

CCP PET-MR funds to sponsor a satellite workshop on Open Source Software for Medical Image Reconstruction at the IEEE Medical Imaging Conference (see ) for details (San Diego, California, from October 31st to November 7th). Details soon but if attending please contact us for details.

31 October 2015 MOSI interactive day with CCPi kiosk and lego synchrotron

30 October 2015 2pm at RAL (VC to DL) Antoniu Pop, University of Manchester, Programming and Optimizing Task Data-Flow Applications with OpenStream and Aftermath Dynamic task-dependent parallelism is an increasingly popular programming model on shared-memory systems. Compared to data parallel loop-based concurrency, it promises enhanced scalability, load balancing and locality. These promises, however, are undermined by non-uniform memory access (NUMA). We show that it is possible to preserve the uniform hardware abstraction of contemporary task-parallel programming models, for both computing and memory resources, while achieving near-optimal data locality. Our run-time algorithms for NUMA-aware task and data placement are fully automatic, application-independent, performance-portable across NUMA machines, and adapt to dynamic changes. We take advantage of data-flow style task parallelism, where the privatization of task data enhances scalability through the elimination of false dependences, and enable fine-grained dynamic control over the placement of application data.In a second part, we present Aftermath, an interactive visualization tool for post-mortem trace analysis of cross-layer performance anomalies in dynamic task-parallel applications. We focus on the detection of anomalies inaccessible to state-of-the-art performance analysis techniques, including anomalies deriving from the interaction of multiple levels of software abstractions, anomalies associated with the hardware, and anomalies resulting from interferences between optimizations in the application and run-time system. Aftermath supports filtering, aggregation and joint visualization of key metrics and performance indicators, such as task duration, run-time state, hardware performance counters and data transfers. While not being specifically designed for NUMA architectures, Aftermath takes advantage of the explicit memory regions and dependence information in dependent task models to precisely capture long-distance and inter-core effects on complex, dynamic applications.


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. 800 participants from more than 40 countries attended the 4-day events including many high quality research paper presentation, 20 workshop, 3 keynote speeches, 6 tutorials and a poster program. If you are interested in the presentations of the three keynote speeches and 6 tutorial, pls go to the conference website to download them the ppts of the three keynote speech presentations: the ppts of the six tutorials

28 October 2015 Informal seminar session on interactive presentations at Daresbury Labs (11am-12noon) "Not yet becoming IronMan? – but software for Touchable Scientific Visualisations" With high-end vis you can (almost) become Ironman (tweet from Laser’s experiment in RAL: but this is not useful for mass engagement and we wished to go beyond videos with simple software solutions to add interactivity. This last year we have looked at open source code, we can use, which replaces commercial codes and allows for the development of touchtable devices but still has high-end graphics outputs. The GPU focussed Prayog system has been chosen, modified and tested at a range of big events; and includes the first purpose built kiosk.

BSSM Meeting at RAL TOMORROW: Tuesday 27 October 2015: 10am-5pm There are places availableto site staff and others. Please email Amanda Boaler directly [] (there is no need to complete the full BSSM [British Society for Strain Measurements] registration form).

BlueQuartz Software in collaboration with LEM3 will be holding a DREAM.3D training course from October 13 - 16 2015 in Metz, France. This 4 day course will cover using DREAM.3D and developing custom plugins for DREAM.3D. Note that the course will be taught in English. Details:

SCD / UoM Seminar 19 October 2015. 3pm-4pm - Video Conferencing Mike Groeber Presentation on the general overview of DREAM.3D" Mike Groeber, US Air Force Overview of DREAM.3D “Analysing Data with Ease” [6.2.0 Released] DREAM.3d an open, extensible software environment to allow integrated processing, characterization and manipulation of microstructure digitally. DREAM.3D is an architecture for computational microstructure tools that allows users to create ‘recipes’ or pipelines for processing digital instances of microstructure. DREAM.3D establishes a robust set of checks and development guidelines to enable singular codes to operate in conjunction, facilitating larger research efforts/goals Software Architecture: DREAM3D is written using many open-source libraries in a layered approach that allows developers and implementors to use just the parts that they want to use. DREAM3D has a robust plugin system where new functionality can be added by developers. The licensing allows for both proprietary and open-source plugins: in R89/Room S48 and room Arkwright in DL and PSI seminar room in the University of Manchester.

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Two day PET•MRI Study Days; 8th and 9th October 2015. This course, supported by Siemens, will provide an introduction and overview to this exciting new technology focusing on the potential clinical and research applications of PET•MRI. Day two is a nahds-on session. Book online at: If you have any queries please contact Lynn Millner,

6 October 2015, 3rd Software Meeting (PET-MR), UCL. Location is Hardy Room, 2-5pm.


5 October SCD Highlights document has a vis section in:


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:

Mantid training Courses 21-23 September 2015 "Following the success of our previous sessions of these training courses we would like to offer them again in September 2015. These courses are open to both facility staff and any interested people from other institutions; Monday 21st September 1-5pm: Mantid Introduction; Tuesday 22nd September 9-12pm: Introduction to Python; Tuesday 22nd September 1-5pm: Python in Mantid; Wednesday 23rd September 9-5pm: Extending Mantid using Python. Booking a place: If you are interested in any other these courses please send an email to letting me know which courses you wish to attend"

Kickoff meeting for the Advanced Radiotherapy STFC Network+ (23 September 2015 in London)

18 September 2015 Brian Bay and Loic Courtois organising a DVC workshop in the Atlas Visualisation Facility (RAL / Harwell Campus)

15 September 2015 CCPi Catch-up session Core Developers

14 September 2015 CFD Unilever-Hartree update meeting Q3 held at Daresbury

7-10 September 2015 University of Manchester A four-day course ideal for Continued Professional Development, with hands-on Open Source CFD Solver training. The course will take place at the University of Manchester with the practical sessions taking place at the Hartree Centre. For more information, a course brochure, and details of how to register please go here…

7 September 2015 CCP PET-MR software developers session at Manchester 12noon to 5pm. At ICAM with webex facilities to other sites.


Poster prize winners sponsored by CCPi at ToScA? 2015


3 september post display involved CCPi winners but we had a few there as well: ULTRA from RAL


3-4 September 2015 ToScA Symposium number 3: held in Manchester (please email questions or if wish to be involved) with CCPi stand:





2 September 2015 4:30pm-5:30pm IVG (Interactive Visualisation Group), update meeting. The Day Before ToScA? : Wednesday 2 September 2015 in Manchester "…to create Touchable Pathways to Impact (and supported initially within the CCPi)"


Joint open workshop in MXIF:


2 September 2015 1:30pm-4:30pm Avizo training course: 2 workflows related to analysis of fibrous materials will be presented. The second use-case is based a PhD student of Philip Withers, Bo Yu, and illustrates advanced usage of Avizo modules for segmentation. Rémi Blanc "Fibre analysis with Avizo" Abstract: The presentation will highlight different usages of Avizo for tackling with fibrous materials. We consider two major use cases. First, in the case of high magnification with resolved fibers, we will present our recent XFiber extension for tracing the centerline of cylindrical fibers and extracting statistics about the length, orientation, or curvature. The second use case will consider woven composites imaged at lower magnification, where individual fibers cannot be distinguished but the oriented texture of the yarns is visible. We will detail an advanced workflow for classifying the yarns based on their orientation. (


2 September 2015 10am-1pm Drishti/Prayog training course - New topics and advanced use within version 2.6 of Drishti including updated version of Paint (release in July 2015;


SCD Newsletter August 2015. Visualisation was involved within two main articles.


MXIF Avizo course will be running from 18th to 19th August 9.30-16.30 (10 places): email ( if interested. Morning session on 18th August will be held at 3.306 at PSI and the rest of session will be at Visualisation Area at HMXIF.

An aside: 1 August 2015, the MOSI in Manchester has 120 games consoles, for public engegement. But visit shows graphics from Pong to Oculus Rift - few million times grapphics increase as about 30 years of Moore's Law.


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

Launch: Avizo (Visualisation software) on Eduserv license Wishlist - "We are all aware of how limited access to commercial software prevents rapid image analysis for many tomography facility users, especially those in other departments/buildings from the scanning equipment. In an attempt to see if FEI would agree to a bulk negotiated discount for academic subscriptions from UK institutions, Avizo has been added to the Chest Software wish list. Many of you will already have access through existing agreements but please, add your support for a Chest Agreement – either complete the online form here or drop Jenny Carrol (jenny.carroll at an email" Kate Dobson. This does not commit anyone to anything - so please vote as more interest will start the process.

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 both around open-source software (ImageJ) and commercial software AVIZO Software course. 28th and 29th of July 2015 at Diamond Light Source. 28th July 2015, Introduction to X-ray Computed tomography. Avizo standard workshop. This will cover loading in data sets, image processing, segmentation and visualisation (ImageJ and Avizo) - 29th July 2015, Introduction to Avizo Fire workshop (quantification). Analysis of inter-connected structures using Avizo and ImageJ. Stephanie C. Masoni Email:

28 July 2015 CCPi Catch-up session Core Developers

14 July 2015 New CCPi leaflet is launched - available in labs and in the ToScA 2015 programme.


13 July 2015 User Survey: To provide better equipment we are doing a survey: "The aim of this survey is to consult with the CCPi (Collaborative Computational Project in Tomographic Imaging - community to identify any current development needs (in terms of equipment, software or personnel), with the aim of aligning these needs with future funding and / or collaboration opportunities."

8-11 July 2015 RAL Campus Open Days: preparation:


11 July Main public day with over 15000 visitors; and ~560 saw fluid flow and molecular visualisation presentations.


10 July Business interests in STFC/SCD

9 July ESA booking for VIP event for presentations

8 July - Schools Visit day; 95 school visitor came to explore 3D space, history of computing on the visualisation wall.


7 July 2015 CCP PET-MR Software Developers Framework meeting in London, UCL

EMiT stand and touchtable use:


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.



29 June 2015 MMC and Team ToScA? Manchester Wing

24 June 2015 The lab hosted its first Nuclear Physics master class;


24 June 2015 CCP Steering Panel included a new version for the touchtable demonstrator.


CCPi reports included touchscreen use: 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 within drishti/parayog (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. The Lego synchrotron was still more popular.


15-19 June 2015 Hartree Vis Summer School


Introduction of Avizo course at manchester; Tuesday, 9 June 2015 from 9.30. Morning session will be held at 3.306 at PSI and afternoon will be at Visualisation Suite at HMXIF. Facilitators are Chris Egan and James Carr. We have 24 places. Would you please email me (

8 June 2015 Unilever Q2 Visualisation for flow session

1 - 7 June 2015 Times Cheltenham Science Festival. Packing up on 29 May 3pm to move and install the maine dinosaur exhibits.


CCPi built touchtables and advertisement at the DinoZone exhibition and helping shift 1000's of posters to 10000's of scientists and future scientists.


29 May 2015 12noon Lego synchrotron design, and 12:30pm Manchester PSI Electron and Ion Microscopy Suite (Greg McMahon) 1pm "Imasim Pro" software overview.


26 May 2015 Team ToScA Manchester Wing Meeting

18 May 2015 CCPi Catch-up session Core Developers

18 May 2015 ICAL workstation - transportartion and demonstration for geosciences

13 May 2015 CCP PET/MR start-up meeting will in London 11.30am-3.00pm


12 May 2015, 9-10:30am Avizo Visit at RAL held in AVF (Atlas Visualisation Facility) R27


SCD Newsletter May: (MJT)


7 May 2015 CCPi Working Group meeting - "Creating a Five Year Plan" Involving a hard-working video-conferencing-lunch across the sites.


followed by different tours at different locations. At Manchester we saw Industrial Tomography in action (bottom left):


5 May Royal Society Phil Trans A., launch of May 2015 Volume: 373 Issue: 2042 "X-Ray tomographic reconstruction for materials science". Prepublicity material is available.


Cover image: High energy, high speed X-ray tomography image of a dandelion flower head. The image was obtained using monochromatic X-rays λ = 0.234 Å (E = 53 keV) at Diamond beamline I12. The complete tomographic series was obtained in 10 seconds as test data for the development of the tomography data processing system. Image credit: Robert C. Atwood. Full articles availble from Journal page:

1 May 2015 MXIF Lunch and Learn; 1pm. "Professor Bill Lionheart will talk about Fast Tomography: From Airport Baggage Scanning to Materials Science. The University of Manchester has recently purchased a Rapiscan RTT x-ray CT Machine, located in the Henry Moseley X-ray Imaging Facility (HMXIF). The RTT110 is capable of producing 3D images in real time, making it the fastest imager in the UK. Currently set-up for airport baggage scanning, we are adapting the machine to utilise its potential for a wide range of experiments, such as granular and multi-phase flows using dynamic x-ray CT. Additionally, Sophia Coban will give a us a glimpse into her paper ‘When do the iterative reconstruction methods become worth the effort?’, which she will be presenting at a conference next month."

29 April 2015 HVM Catapult Applied Immersive Visualisation Event – 29th April at the AMRC, Rotherham Supported by the KTN and National Technical Committees for Synthetic and Simulated Environments and Human Factors


28 April 2015, Developers' Day at Manchester Workshop to focus on iterative solutions for the XTek machines (such as the released CGLS code) and what is required to get them into regular usage in the labs that use these machines. 11am-4pm.


Followed by a tour of the new Henry Mosely X-ray imaging facility;



27-30 April 2015 Physics & Software PET-MR training school this April in Leeds. If any early stage researchers wishes to attend (Masters, PhDs, or Post-Docs) might be possible to attend for free if they express their interest on time (UK-affiliated researchers are welcome to apply).

24 April 2015 CCPi Show-and-Tell 'Avizo VR - Tomographic Vis with full tracking and interaction' from 2pm in Atlas Visualisation Facility


With tweet from Ceri Brenner @CeriBrenner:


22-23 April 2015 SCD Away Day - includes a poster on Vis Group activities:


and an emot-visgroup slogon. Test version here:


Training 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 both around open-source software (ImageJ) and commercial software AVIZO Software course. This is the fourth training course of this kind to be offered by the Diamond Manchester Collaboration and will be on the 16th and 17th of April 2015 at Diamond Light Source. The course will consist of a lecture and hands-on exercises intended for new or existing users of Avizo software. Attendee capacity for the training is limited to 25 so if you are interested please register with me at your earliest opportunity. As we are also training future trainers, people volunteering to help in future courses will be given priority.

1 April 2015 CCP PET/MR kick-off event in London

27 March 2015 Software-show-and-tell in RAL - Image processing software, NOCTYlab, show-and-tell from NOCTYLIO ( "Noctylio is a software start-up company located in Bordeaux; its purpose is to open up new horizons in 3D imaging"

26 March 2015 HPC@Sheffield "Global Grand Challenges Day" - Visualisation Matters the need to put the human back in the imaging-capture-and-computational loop: Subtitle: case studies from work with the Hartree Centre, CCPi ( ) and the Harwell Imaging Partnership as well as future opportunities for collaboration and resources. Dr. Martin Turner, STFC, Hartree Centre, Scientific Computing Department. A pdf file is available of the images: Hartrer_Sheffield.pdf

24 March 2015 Developers' Day for CCPi on Touch Table integration and use; at the University of Reading.



18 March 2015 "CCPi core" developers' update session 4pm Pre-session in new x-ray labs before.

17 March 2015 Team ToScA? - Manchester Wing video conferencing session

9 March 2015 -> for three to four weeks, HPL Vulcan access for image acquisition

Diamond and ISIS have a CDT doctoral training working shop in 9-13 March 2015. On 9 March there will a one 2h introduction and a 2h training session on imaging and visualisation. Contact Winfried Kockelmann

Q1 Unilever UK Innovation project meeting in Manchester


SCD Seminar 27 February 2015. 3pm-4pm: Friday 27 February 2014 - "Fast Tomography: From Airport Baggage Scanning to Materials Science" Nicola Wadeson, CCPi Visiting Scientist at Diamond @Room S44 in R89 at RAL and Video conference to Arkwright room in DL. The University of Manchester has recently purchased a Rapiscan RTT x-ray CT Machine, located in the School of Materials' Henry Moseley X-ray Imaging Facility (HMXIF). The RTT110 is capable of producing 3D images in real time, making it the fastest imager in the UK. Currently set-up for airport baggage scanning, we aim to adapt the machine to utilise its potential for a wide range of experiments, such as granular and multi-phase flows using dynamic x-ray CT. This will be at 3pm at Rutherford Appleton Laboratory on the Harwell Campus: in R89/Room S44 and room Arkwright in DL.


... There will also be an update on the ICP (IMAT Computing Project) – IMAT is the first neutron imaging instrument at ISIS; the first of its kind in the world offering unique time-of-flight tomography-driven diffraction techniques; and will link to SCD computational facilities. Lead by Erica Yang

Lunch and Learn will take place on Friday 27 February, 12:30pm, at the ICAM seminar room. Dr Martin Turner will be giving a presentation on “Visualisation Matters - the need to put the human back in the imaging-capture-and-computational loop: case studies from work with the CCPi ( and Harwell Imaging Partnership as well as future opportunities for collaboration and resource". I n case you can’t join us at Manchester, the presentation will be broadcasted through

Thursday 26th February in the VEC VR Lab commencing 10.00am - Visionary Render training course with VEC

17-20 February 2015, Developers' Day at Manchester supported by CCPi - "Avizo developement - Module integration - Reconstruction techniques - Image processing" four day workshop: ICMCB-CNRS: CCPI: MXIF: UOM - Maths: AVIZO: AMARI: Diamond I12


Mantid Training Courses Feb 2015. The following courses will be based at ISIS, RAL and are: Monday 16th February 1-5pm: Mantid Introduction An introduction to the Mantid interface, how to graph and visualize your data, manipulate it with the built in algorithms, together with an introduction to curve fitting and live data analysis. Tuesday 17th February 9-12am: Introduction to Python This half day course will introduce you to the Python scripting language, no previous experience required, although some understanding of loops and conditional if statements will be expected. Tuesday 17th February 1-5pm: Python in Mantid This course concentrates on using Python to build analysis scripts within Mantid as well as controlling the Mantid GUI from python, and accessing the underlying data within Mantid workspaces. Wednesday 18th February 9-5pm: Extending Mantid using Python For the more adventurous among you this course will introduce you to the many ways you can use Python to extend the capabilities within Mantid adding Python Algorithms and curve fitting functions, as well as diving deeper into the structure of workspaces. After the feedback from the previous run this course has been extended to a full day course, together with adding more material. Booking a place If you are interested in any other these courses please send an email to

EPSRC SoFT kick-off meeting 11 February 2015.


Related SCD Session: 11am: 13 February 2015 - Talk by Prof. H. Jasak and Dr G. Tabor in Cockcroft Walton Room A DL & VC Link to S48/R89 RAL.

This was video recorded and available: "OpenFOAM at Exeter"; Gavin Tabor CEMPS

WP_20150204_001_cs.jpg 'OpenFOAM and FOAM-Extend: Overview of Capabilities' OpenFOAM® (Open Field Operation and Manipulation) is an open source Computational Fluid Dynamics (CFD) software, which is widely used in both academia and commercial organizations. This seminar will be delivered by two of the most prominent members of the OpenFOAM community in the UK, Prof H. Jasak and Dr G. Tabor. The first part will review the numerical capabilities of OpenFOAM with a particular focus on an enhanced released of the software name FOAM-EXTENDED particularly for multiphase and moving mesh type of calculations. The second part will be devoted to the review of some recent applications performed at the University of Exeter in the field of Suitable Urban Drainage, Tidal renewable energy and compact 3D printed heat exchangers. Some details about Image Base Meshing will be also given. Friday 13 February

11 February IMAT demonstrator day to ISIS management - work managed by Erica Yang: ICP (IMAT Computing Project).

2 February 2015 Survey site for Visualisation User Needs launched


Sakai banner image: See Rob Allan regarding login etc.sakaibanner.jpg

15 January 2015 CCPi update session and user needs visualisation update.

14 January 2015 - CCP Steering Panel with Touch Table demonstrations of varions CCP related visualisation software.


Merry Christmas and Happy New Year: The Visualisation Labs is Miss June on the STFC Photowalk Calendar 2015.


19 December 2014 Awareness raising event for VEC and Hartree based around the hosting of UoL's Formula Student Sponsors day


19 December 2014 - Postponed ... in Manchester's ICAM (Pariser building), Prof Jonathan Blackledge from South Africa

18 December 2014 Tomo-and-Coffee session for visualisation needs survey results. Presentation at CCP_survey_plus.pdf and wiki at:


16 December 2014 NPG Presentation on a range of topics with a section on visualisation "Visualisation Matters - the need to put the human back in the computational loop"


12 December 2014, Tomo-and-Coffee Pre-Christmas talk: RAL in at RC@H (rooms 1 and 2): Prof Sarah Hainsworth, University of Leicester. Sarah Hainsworth will be talking on "Forensic Applications of micro-computed tomography; Bones, flies and Richard III". Sarah has a BEng and doctorate from the University of Newcastle and is a Chartered Engineer (CEng), Chartered Scientist (CSci), and a Fellow of the Institute of Materials, Minerals, and Mining (FIMMM). She was the recipient of the Institution of Mechanical Engineers Tribology Bronze Medal in 1995, the Rosenhain Medal of the Institute of Materials, Minerals, and Mining in 2008, and was nominated as one the Women's Engineering Society's Outstanding Technical Women in 2009. In the area of forensic engineering, research is into two main areas, forces involved in stabbing and characterising tool marks in injury and dismemberment.


(Video Recorded on SCD streaming server - click on image above for link).

9 December 2014 Main CCPi Working Group Steering Panel


4 December 2014 - Autumn Statement resulted in demonstrators, for Graham Evans MP (Weaver Vale) et al. - this demonstration one from Roger Downing mapping geospatial data for IBM.


2-3 December MEW 25 -- and talk about visualisation in SCD updates breatout section 2-4pm 3 December 2014 "Visualisation Matters - the need to put the human back in the computational loop"


1-4 December 2013 - setup and event for University of Liverpool: involving all spaces of main room as well as side rooms.

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.

1 December - visitors for full tour and collaboration.


Coffee-and-Tomo Session: Wednesday 26 November 2014, Demos 2pm-3pm in DL and 3pm-4pm Speaker: Sam Worthington (Worthington Sharpe Ltd.) "Wing: Beyond the mouse". The Wing combines full 3D control with the precision of a professional laser mouse. It is initially designed to meet the demands of Uninhabited Aerial Vehicle and Remotely Operated Vehicle control, Computer Aided Design software, Virtual Reality, and simulation or training games. The Wing is ideal for any application requiring the speed and accuracy of a high-end mouse, as well as free-flowing and intuitive 3D interaction.


19 November 2014, GSK session and seminar

18 November 2014, CCPi update meeting

13 November 50 Years of Atlas that included CCPi visualisation showing the advancement from the "graphics of the 70's".



The Cryo-Ops 2014 held was big success with 93 people viewing- although in three sessions. November 12, 2014


10 November JPEG2000 Meeting Welcome Trust in London

SCD Seminar on Tomography Bill Lionheart, University of Manchester 2pm, 6 November 2014. Location: CR03, Rutherford Appleton Laboratory (CR4 @ DL) "Tomographic problems as linear algebra" For many tomographic imaging problems there are explicit inversion formulas, and depending on the completeness of the data these are unstable to differing degrees. Increasingly we are solving tomographic problems as though they were any other linear inverse problem using numerical linear algebra. I will illustrate the use of numerical singular value decomposition to explore the (in)stability for various problems. I will also show how standard techniques from numerical linear algebra, such as conjugate gradient least squares, can be employed with systematic regularization compared with the ad hoc use of slowly convergent iterative methods more traditionally used in computed tomography. I will mainly illustrate the talk with examples from three dimensional x-ray tomography but I will also touch on tensor tomography problems. For further information, contact Tyrone Rees (


SCD October Text: The annual Tomography for Scientific Advancement (ToScA? ) Symposium, 1-3 September 2014, was hosted at the Natural History Museum, London, UK. Where SCD’s CCPi (Collaborative Computational Project in Tomographic Imaging, actively contributed to keynotes, speakers, workshop discussion, ran an exhibition stand as well as sponsored the student poster competition. This was an opportunity to iron and clean the STFC tablecloth from Media Services; as well as dust off the YouTube? video collection ( (MJT)

scdOctober2014.jpg There was a lot of hard work in seminars and networking, including student prize judging around the museum artefacts and we were joined for the evening dinner with Dippy. Dippy is the affectionate name for the diplodocus skeleton cast that is often the first sight to greet Museum visitors first unveiled in 1905. As expected in the basement of the NHM there are plenty of artefacts and less expected many scientific imaging devices; including a range of SEMs and importantly for STFC a Materials Science X-ray CT (Computed Tomography) machine (Nikon Metrology XTek 225); doing small scale laboratory based work similar to Diamond Light Source beamlines i12 and i13.We extended one of the keynote hospitality, Dr Ajay Limaye, with a short-term CCPi Fellowship, by later in the week having him present a training course in the morning followed by a visualisation data needs workshop in the afternoon; at RAL in the Atlas Visualisation Facility, on the open-source Drishti volume visualisation system, (MJT - Martin Turner

Python Community of practice 2 (PyCoP2) run by CCPi WG member Mark Basham “Community of Practice” event targeting Python which is used widely around the RAL Site; 31 October 2014.

30 October 2014: DL Open day including historic computers

Outreach event showing new network visualisation tools, 23 October 2014


22 October 2014 - planned Developers' Workshop: CCPi Released a executable based on code from the University of Manchester that uses the iterative CGLS algorithm for image reconstruction from XTek CT systems. The defaults in the interface should provide reasonable initial values. A full resolution reconstruction will use ~128GB and depending on your system can take a few hours per iteration. The project page on CCPForge is


Coffee-and-Tomo Session: 3pm-4pm: 10 October 2014 - Talk by Russell Garwood in R89 (S44)

WP_20141006_001_DxO_cs.jpg Open source software for visualising tomographic datasets: Russell Garwood; University of Manchester. “This talk will provide an overview of free and/or open source software for processing and visualising tomographic datasets. It will be followed by a discussion of other software/tools for performing quantitative analysis of this data. One of the greatest weaknesses of open source packages available - or indeed my knowledge of what's out there - is a lack of free tools for quantifying tomographic data.“ R89/ room S44. If lost or unsure please email:

This was the first Vis talk that was recorded as well:


We did a Voluminous NCI VizLab demonstration showing remote volume visualisation in action from Australia (time on video: 39:12).


Introduction to the Software Engineering Support Centre and CCPForge one-day Workshop at RAL 7 December 2014

Coffee-and-Tomo Session: 3pm-4pm Friday 26th September 2014 "Image-based simulation of diffusion and flows within experimental volumetric data sets Dr Marcus Campbell Bannerman, University of Aberdeen" in Seminar in R89/S44 Combined as an SCD Seminar.


IMG_9640_cw.jpg 26 September 2014 SCD Seminar With the proliferation and availability of X-ray imaging facilities, the size of volumetric data sets and their rate of collection has increased by orders of magnitude in recent years. The manual reconstruction of these transmission images, image analysis, and extraction of indirect information through simulation is rate limiting as it requires extensive user input and experience. In order to remove this barrier, and to provide the additional benefit of image-based modelling, we believe the integration and automation of a “data pipeline” is required and this is the focus of a recent EPSRC sponsorship award (EP/L026716/1).

The first part of this presentation will introduce some early work on a new mesh-free method for statistical simulation of molecular flows within the domain of an imaged pore-space. This work uses the DynamO code ( and overcomes the difficulty of automated mesh generation by directly using the image data-set as the domain of the simulation. This allows a time-to-simulation of the order of hours rather than days for extraction of parameters such as anisotropic diffusion coefficients. The second part of the talk will present the visualisation library of DynamO. This software allows the real-time visualisation of large (N=10^6) systems of particles and volumetric data using a variety of techniques (instancing, bill-boarding, ray-tracing, HDR). Both topics are presented as works in progress, so feedback with vigorous debate and discussion is welcome and highly encouraged! This will be at 3pm in S44 room in R89.

SCD Newsletter Highlights Brochure: Visualisation Group entry, draft release 25 September 2014 so pre-print below (open in new tab for higher resolution).


UoM: HMXIF Courses 8-12 September 2014: Introduction to X-ray Computed Tomography (XCT) and AVIZO standard on the 8th Sept. AVIZO Fire – advanced characterisation of discrete features such as precipitates using AVIZO - 9th Sept. Analysis of interconnected structures such as complex porosity structures using AVIZO, ImageJ and MATLAB - 10th Sept. 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 – 11th Sept. For advanced users, collaborators and industrial partners of the HMXIF only (please contact HMXIF staff for this course) 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 – 12th Sept.

10-11 September 2014, Eurographics UK Chapter event in Leeds. Acted as nvidia accademic link for sponsorship.


Young Researchers in Image-based Modelling 9 September 2014 'Postponed'.

CCPi Short-term fellowship visit: Drishti 2.5 was released on 27 July 2014, and on Monday 8 September, Ajay Limaye is arriving at RAL to give a workshop and discussion of the features. ( Latest Code: Email Sri ( or Loic ( to book a spot - being held in RAL, please email as limited space.

Previous show and tell at the NHM...


...followed by workshop at RAL the following Monday morning and a data analysis hands on session in the afternoon.


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


With the student poster display:


and then dinner with Dippy:


Tour of the CT and other machines in the basement of the NHM 3 September 2014


ParaView type Meeting 28 August 2014: A branded ParaView-based application, called tomviz by Marcus D. Hanwell et al.: "with focus ion STEM tomography at atomic resolutions for materials, but it is also exploring how to make a focused application that enables visualization and analysis of volumes: Developing the concept of data processing in Python to enable researchers to easily develop new data analysis, reconstruction, and transformation techniques leveraging things like numpy. It was presented at M&M two weeks ago, and we will be adding some alignment and reconstruction capabilities in the next release."

WP_20140820_001_DxO_cw.jpg 27 August 2014 SCD Seminar hosted by CCP5/BioSIM: "Avogadro 2: Scaling to Large Systems, Improving Code Integration and Chemical Data Informatics/Analytics" Avogadro 2 is a complete rewrite of the Avogadro project, with a suite of targeted software libraries, and an end-user application all permissively licensed under the open source BSD license. Everything from core data structures, file input/output, and rendering have been rewritten with an emphasis on extensibility and scalability while maintaining usability. Avogadro 2 has been demonstrated interactively rendering large systems with in excess of 2.8 million atoms, and small quantum results using volume rendering for electronic structure among other techniques.

Next video conference using IBM Meeting system and Skype along with curved wall visualisation with numerous VMD output images.



Video Conferencing between the sites: tests using visimeet have started and produce reasonable results: Initial session on 8 August 2014, involved visualisation for London Underground monitoring project being carried out at RAL.


WP_20140729_001_DxO_cw.jpg 1 August 2014 SCD Seminar and visit by Dr Helen Wright, from University of Hull; at RAL 11:00 hours Location: S44/R89 RAL via VC Link to Arkwright A23 (2nd Floor) DL Developments at the Hull Immersive Visualization Environment (HIVE) "HIVE was established in 2002 using SRIF funding, to provide advanced visualization and virtual environment research facilities to the University of Hull and its industrial partners. The philosophy from the outset was to have a variety of facilities that could be adapted to the different needs of diverse applications. The flagship installation is the 5.3m X 2.4m back-projected wall of HIVE's 30-seat auditorium, with active stereo and optical (infra-red) head-tracking system. HIVE also has several front-projected passive stereo systems (both fixed and portable for outreach activities), a personal immersion dome, inertial full-body tracking, and various haptic displays and head-mounted displays.

The auditorium optical tracking system also extends out beyond the stage into the audience area so by clearing the seating can provide a 5m X 10m space for large-scale motion capture. HIVE is based in the Department of Computer Science and, in addition to its wider role within the university and beyond, houses the research infrastructure of the department's Simulation and Visualization Research Group. This talk, by the group's leader Helen Wright, and HIVE's Acting Director, Warren Viant, will describe recent developments in this infrastructure, notably a 4-sided 2m X 2m X 2m immersive projection 'cube' built in-house in 2013, and a new 4.5m X 2.4m x 3m walk-up/walk-on visualization volume. This utilises the auditorium's back-projected wall, extended into an L-shaped display by the addition of floor-projection over the majority of the raised stage area. Our talk will include some of our recent and forthcoming projects, ranging from close-to-market prototypes with an industry focus, to fundamental empirical science helping understand our perception of synthetic space."


Coffee-and-Tomo Session: 1 August 2014 Morning session 2pm-4pm- Bring your own data Tomo session II.


FOT Young Rewired State event - for future hackers and developers; 30 July 2014

28 July 2014 Vis plays a role for the new University, Science and Cities Minister


21-25 July 2014 and 27 July - 1 August 2014 Hartee Summer Schools. Includes demos (a few too many people crammed in the room) as well as use of delegate's data



Tweets from Hartee and others:


22 July 2014 CCPi Third Developers' Workshop held at Nottingham's Hounsfield Facility; a multi-CT-machine with novel robotic-greenhouse attachment.


14-18 July 2014 Hartee Summer School in Visualisation that was has also been tweeted by : Matthieu Chavent @Matth_Chavent Researcher, Molecular Visualization, Biophysical Modelling, Biological Complexity viscourset.jpg

Avizo visualisation course at the Diamond House, 16-17th July 2014; via the RCaH/Diamond Consortium

4 July 2014 Prof. Andre Phillion, from UBC, will be visiting RCaH on Fri July 4th; Seminar Meeting rooms 1+2; 1:30pm "3D Imaging and Simulations of Complex Fibrous Materials: Applications to paper-based products and fiberglass/polymer composite yarns" A.B. Phillion, Y. Sharma, M. Targhagh, M. Mohammadi

3 July 2014 evolution of HIP

Dr Brian Bay CCPi Fellowship Tour: @ UCL 3 July 2014 for a mini-conference (10am-5pm) then UoM and Oxford

2-3 July 2014 Information visualisation workshop in Oxford: Hosted by Prof Min Chen at the OeRC (Oxford e-Reseach Centre). This meeting was based around Biological visualisation focussing on Information Visualisation techniques. Keynote visitor was Tamara Munzner from the University of British Columbia.


SCD July Text: 23rd April 2014 - Filming for the Liverpool Business Community Turning the visualisation suite into a film studio, we at DL have played a small part in the STFC Filming session, 'Sci-Tech Daresbury Shoot' for the International Festival for Business Visualisation rooms were used for a session as well as outside locations, including recording of Dr Massimo Noro from Unilever describing the research partnership that exists between the sites through the Hartee Centre. The films are being shown within the festival in Liverpool held June-July 2014. Massimo Noro, Unilever with film-crew, at the Daresbury Labs., Hartee centre Crosfield Visualisation Room. Thanks specifically to coordination inculding Hartee and Rob Allan from SCD; as well as all those who worked hard behind the scenes (MJT)

scdJuly2014.jpg Exhibition stands for CCPi/HIP/SCD – visualisation integrates with the facilities. Starting with supporting the Materials KTN with their Intelligent Imaging Programmes in 2013; we have now a combined stand for CCPi, HIP and SCD. Recently we have had stands at the main Materials KTN Materials Research Exchange 24-25 February (Ricoh Arena, Coventry) and the EuroVis 2014 conference, hosted by Swansea University in the UK, in 9-13 June 2014. This latter event (photo below) was the 16th annual visualisation gathering organized by the Eurographics Working Group on Data Visualization and supported by the IEEE Visualization and Graphics Technical Committee. The stand is there to promote the HIP (Harwell Imaging Partnership), CCPi (Collaborative Computational Project in Tomographic Imaging), Hartee Centre and related facilities including ISIS and Diamond. Essential for this are the SCD/STFC pull-up banners, posters and of course the new labelled table cloth. Each of the last two events had a few hundred delegates and both times we ran out of STFC/SCD annual reports (MJT - Martin Turner

So we can host 45 people in the Leverhulme visualisation suite - semi-comfortable but not recommended. This was a group of German students hosted by the North West Training Council on 27 June 2014.


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, on the Hartee systems, with tomographic 3D image capture; and add the human-in-the-loop. This two year project is planned to start in September 2014.


Coffee-and-Tomo Session: 26 June 2014 - update on Diamond Light Source DAWN data flow system. First one using the bluejean video conferencing system to DL. Next time go on to Manchester and beyond. View from DL end.


24 June 2014 Big Data Day at the International Festival for Business. Both generic and general visualisations were presented; this one carried out by David Moss


and another by Adrian Toland at the Daresbury Breakfast show on 27 June 2014;


... as well as more fun social-media activities. The social-media tagline is #opportunity; so Opportunity Arrives at STFC


17-18, 23, 25, 30 June 2014 ParaFEM update sessions

17 June 2014 CCPi Working Group Meeting held at the Atlas Visualisation Facility


EuroVis 2014, hosted by Swansea University in the UK, 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



We are about to launch a new website so visit us through SCD:


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 Course will start on day 1, in the HMXIF laboratory then in BP-ICAM.

10 June 2014 CCP SP Meeting at MRC.

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)

We carry out many VIP demonstration sessions; including this one on 4 June 2014, by Rob Allan to Tim Sherwood Chair Satellite Applications Catapult and Rob Douglas Chariman of the Steering Board for UK Space Agency.


Coffee-and-Tomo Session: 30 May 2014, general discussion and overview of volume visualisation within ParaView compared to Drishti, Slicer 3D and Avizo.


21 May 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.



20 May 2014 CCPi Second Developers' Workshop held at Birmingham

13 May 2014 IMechE? event

8 May 2014 Avizo 'experts' workshop was held at RAL considering use of v8.1


7 May 2014 OpenFOAM workshop from a set, included a presenattion by Ron Fowler on client-server statistics of ParaView operations as could be used within OpenFOAM. Followed on from a 1 May OpenFOAM developers day.


6 May 2014 Big Data Meeting in RAL; also events on 10 May in SCD/DL and Media City. Hartee's BDM Lee Hannis presented at this meeting, but also included a network visualisation system from BBSRC.


2 May 2014 Software demonstratiuon by Thomas Salvini from that turned our curved wall into an ipad-mini controlled dashboard for selected and changeable visual analytics output. Initial test with the Clarity3 software in its vanilla format.


24 April 2014 Our TSB Project with a visualisation component has been approved within the Towards Zero Prototyping programme. The introduction by Paul Tuffs within the New Projects Workshop session to go through the bureaucratic reporting and costing system was going so well until he showed the reporting information pathway graph. Should be a good project and see outcomes here in the next two years.


23 April 2014 - Filming session, 'Sci-Tech Daresbury Shoot' for the Liverpool Business conference. Visualisation rooms were used for a session, including recording of Massimo Noro from Unilever describing the research partnership that exists between the sites.


_Postponed_ Second CCPi Developers' Workshop 22 April 2014 CCPi developers only day focussing on reconstruction and DAWN

SCD were commissioned by Dr Jon Blower, in Reading University for software setup and assistance in building their new tiled touch-screen videowall. Utilising a single glass front surface covering 8 large LCD panels, it is a single touch-display surface which they will be using to do their data presentation on; installed and completed on time by end of April 2014.


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 )

8 April 2014 !ParaFEM visualisation initial layout and analysis day with continuation on 14 May 2014. Blogged on


The raspberry-pi on the large screen: thanks to Daniel Barker from @4273pi for a great SCD talk, 7 April 2014 and demoing the system running BLAST


31 March-1 April 2014 Virtalis Filming Proposed (pre-session 24 March 2014). Rupert Ford presenting novel modes of operation for the Gung-Ho project to design and build a next generation weather forecasting model for the UK (collaboration between the Met Office, NERC and STFC being one of the first major projects to benefit from the Hartree Centre).


... Terry Hewitt employing ActiveView allowing multiple laptops and tablets to be used within the same presentation


... Anthony Gleeson describing the VERA accelerator model within the fully tracked VEC power wall


... Stefano Rolfo showing a 3D CFD model integrating Code_Saturne output from the Hartee GPFS onto the main curved wall


... Andy Connell demonstrating the power of integrating, movable laptop video streams within a 3D presentation; mixing visual modes using ActiveView


... Iain Cant and Louise Wang driving the VR Formula Student model from the University of Liverpool, using the Visionary Render software CAD viewer.


Coffee-and-Tomo Session: 28 March 2014 Digital Volume Correlation (DVC) from LaVision - a novel tool for quantifying full-field displacement and strains; Dave Hollis from LaVision


27 March 2014 IMechE evening event - all run by the DL guys but stats were refturned from the feedback. "69 people registered interest in attending the event. 51 people actually attended the event. 36 people completed feedback forms, of which 16 reported event fully met expectation. 19 reported event was above expectations. and 1 reported event greatly exceeded expectations."

25 March 2014 TSB Space Applications Catapult centre launch event for a new command and control centre. Panorama picture (below) was captured a month later (25 April 2014) while testing a shipping monitoring system.


Paraview Forum (DL) 19 March 2014 Paraview and Related Vis Tools Forum; from a Paraview and Coffee (DL) pre-session 5 March 2014 discussion over lunch in away-day with Technology Division and VEC

WP_20140320_005_DxO_css.jpg Paraview and Coffee (DL) 19 March 2014 Paraview and Related Vis Tools Forum – First session at Wednesday 19 March 3pm. Held in DL, and try (visimeet) VC to RAL: Forum for Paraview users – initial round table discussion. There is a growing interest within a diversity of groups within SCD, wider STFC and partner organisations like the VEC, aimed at integrated computation and visualisation processes. A common platform is the ParaView environment It is proposed to have a monthly forum to share experiences and practice to help old hands and encourage new novices. The facilities at the Hartree centre, visualisation and compute, are available for certain demonstratable experimentations and already have a range of paraview versions installed in a variety of configurations.

International Bioenergy Conference 11-13 March 2014 - STFC presentation, including Vis and HPC


Paraview and Coffee (DL) pre-session 5 March 2014 Discussion over lunch in away-day with Technology Division and VEC

Coffee-and-Tomo Session: 28 February 2014: Jon Taylor (ISIS), Mantid project provides a framework that supports high-performance computing and visualisation of scientific data. The framework is open source and supported on multiple target platforms (Windows, Linux, Mac). (


27 February 2014 Visit SuperSTEM/STFC Laboratory Atomic scale imaging and spectroscopy/”STFC contribution(s)”


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"


Not visualisation but a stand from Rob Allan and Tim Franks, very minor role in history stand - but gave visualisation demos to other stand exhibitors and BIS representatives. Also the start and middle to Atlas 50 celebrations:


Data workshop for Diamond/ISIS/SCD 17th February 2014 Diamond House, G59; with visualisation needs covered.

Coffee-and-Tomo Session: 31 January 2014 NIRFAST: An interactive GUI driven toolbox for modeling and image reconstruction in optical imaging" Hamid Dehghani.


Q&A with a Senior Cabinet Minister Satellite Applications Catapult, Electron Building, Harwell Oxford Campus Thursday 30 January 2014 (13.20 - 13.50). Other MPs have include local MPs and opposition Minister.

MXIF Two day training - Introduction to Avizo Fire workshop. 29 January 2014 and - Introduction to X-ray Computed tomography. This will cover how XCT works, introduction to reconstruction, reconstruction artefacts, Image processing etc. and Avizo standard workshop. This will cover loading in data sets, image processing, segmentation and visualisation. 28 January 2014

RCaH Training Course in CT and Avizo 27 and 28 January 2014

CCP Forge meeting 16 January 2014 held by our colleagues in SE

Training in CT and Avizo at DLS (RAL) 15-16 January 2014

CCPi Developers' Workshop 14 January 2014 First CCPi developers only day including interation with CCP ASEArch.


Merry Christmas and Happy New Year:

rotr_p4651-4669p40_vs_1.jpg rot_p4651-4669p40_vs.jpg

Coffee-and-Tomo Session: 20 December 2013 - Bring your own data Tomo session.



SCD Seminar on HIP Harwell Imaging Partnership; on 18 December 2013, 10am Mike Curtis-Rouse and Joe Kelleher at RAL will describe some present and some future interactions between the Harwell Imaging Partnership and SCD.

IMG_9389_cs.jpg "SCD Interactions with the Harwell Imaging Partnership" The Harwell Imaging Partnership (HIP) was established to promote industrial engagement with STFC large facilities by fostering interactions between industrial researchers, STFC facility scientists and university research groups. In this context, “imaging” includes microscopy, tomography, and ‘functional imaging’, in which properties of complex structures are mapped with high spatial resolution using X-rays, neutrons or lasers. SCD is being considered actively as a ‘facility’ in its own right in this context. A set of case studies based on data transfer, portal interaction, remote access including computation, as well as visualisation specialisms have all been added to the HIP portfolio. This introductory short session will cover some of the opportunities available by working with the HIP as well as future proposed new centre interactions.

Awareness raising event for VEC and Hartree based around the hosting of UoL's Formula Student Sponsors day 13 December 2013


12 December 2013 - picture of pre-setup for University of Liverpool event: included all spaces of main room as well as side rooms (not shown).


SCD Seminar: GPU Whales on 10 December 2013, 3pm; Dr Longshaw is from the School of Mechanical, Aerospace & Civil Engineering at the University of Manchester and is a member of the Smoothed Particle Hydrodynamics Expert Group. He completed his PhD in Computer Science at the University of Manchester in 2011 with a thesis that explored the use of novel computing hardware, such as GPUs, and associated software frameworks to solve demanding numerical simulation problems such as Discrete Element Modelling and Smoothed Particle Hydrodynamics.

WP_20131206_001_DxO_cs.jpg Stephen Longshaw, University of Manchester "Whale to Turbine Impact Simulated Using CUDA Based Smoothed Particle Hydrodynamics on GPUs" As underwater turbine farms to harvest tidal energy become a reality, a key question is what effect will they have on their surrounding environment. This work, as part of the EPSRC funded X-MED project, aims to model the macroscopic effects of a Minke whale impacting a rotating turbine blade whilst submerged in water. To achieve this, a new method that integrates a particle based elastic model directly with the Smoothed Particle Hydrodynamics (SPH) method has been developed. Due to the computational demand of SPH, combined with extra overhead introduced by the elastic behaviour, this work has been achieved by extending the CUDA and OpenMP based DualSPHysics SPH simulation software (a joint development between the University of Manchester, UK and the University of Vigo, Spain).


Training course on Digital Volume Correlation in RAL, with Brian Bay from LaVision 10 December 2013

SoFT project launch at RAL; 9 December 2013, 11am to 5pm


Coffee-and-Tomo Session: 29 November 2013 Quantification Visualisation event - request for problems, (held at RAL).


MEW 27-28 November 2013

VisionaryRenderer from Virtlais - initial software show in VEC 27 November 2013


JISC VRE Calls with reference to hartree setup 20 November 2013

SCD Seminar on Accelerator Technology on 19 November 2013

WP_20131115_001_DxO_cs.jpgCCP ASEArch - Investigating Algorithms on Multicore Architectures: host David Worth. Tuesday 19 November 2013 at 2:15pm Arkwright, A Block DL & VC Link to CR12 RAL. Algorithms and Software for Emerging Architectures (ASEArch) is an EPSRC-funded Collaborative Computational Project (CCP) which has as one of its main tasks to investigate the performance of core numerical algorithms on multi-core processors, such as Intel x86 or BlueGeneQ, many-cores accelerators, such as GPUs, Intel's Many Integrated Core (MIC), and their hybrid combinations used in the latest HPC architectures. This seminar provides an overview of the work being done by the CCP-ASEArch and provides background information for future interactions with CCP-ASEArch.

Atlas Visualisation Facility - initial launch and descriptions within the SCD November 2013 Newsletter:


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. Note need a bigger laptop screen - as the Diamond i12 experiement video had a lot of interest. (see the ccpi youtube site).


Training Course at UoM: Avizo with SCD staff 29 October - 1 November 2013

Fly-through demonstrator - using a converted player we can in stereo (so images slightly blurry) see the ALICE-EMMA (Accelerators and Lasers In Combined Experiments test accelerator designed and built at Daresbury Laboratory) in VR. There are plans for an up to date conversion.

p131028_4-8p40cbs.jpg p131028_9_cs.jpg

with an internal CI Particle Accelerator School 'show', 4 November and 14 November 2013.


Coffee-and-Tomo Session: 25 October 2013 This was a great little session exploring joint experience of the open source Drishti volume visualiser that is taking the community by storm. Pros and cons were discussed over cookies.


Mixed training all in one day 23 October 2013 - from BlueGene/Q Advanced Training and Optimisation Course at one end of the corridor to Raspberry Pi training at the other end - with similar concepts. We can provide interactive training examples for both.

First seminar SCD Seminar to start a forum across the sites: Relighting and Beyond on 14 October 2013

poster_1_cs.jpg Mashhuda Glencross, Loughborough University "Relightable Buildings from Photographs and Beyond" In this talk Mashhuda will describe previous work at Loughborough University on creating perceptually high quality 3D reconstructions of real outdoor scenes. She will also outline more recent work to build a material reflectance acquisition setup, and how this setup will be used to study material perception. Mashudda will conclude with the requirements for perceptually validated material models within the automotive industry, outlined in a recent industry position paper. Monday 14 October 2013 at 2pm Arkwright, A Block DL & VC Link to R89 Seminar Room, S44 RAL

SAFER test connection to Chile, TSB Space Catapult, 10 October 2013. See their news feed and flickr pictures.


(link photo from flickr site).

Training course in 3DVIA Studio Pro over 8-10 October 2013


Included a VC session on use-case scenarios; and there was a training course in Avizo 7-8 Oct 2013, at RCaH.

CCPi Mid-term Review, 30 September 2013 - document to appear also in a SCD Highlight article (link to appear soon).


This image is a screen capture from the 15mpixel curved wall (8025 x 1920 pixels)., open image in new tab to zoom in - ideal for layout and is then perfect resolution for a published article.

The CCPi published article is:


SCD Highlight Visualisation showing multi-software simultaneous 3D visualisation to highlight different scales and aid in comparisons:


Coffee-and-Tomo Session: 27 September 2013

TotalView steering challenge - could the rooms be used for debugging and monitoring. This request came from the training day held on 24 September 2013.


Code_Saturne CFD Week Course, 8-13 September 2013. First cross comparison and computational link to BlueGene and Paraview - not in real time yet.


Stefano Rolfo and Charles Moulinec presenting and running cfd code in the Hartee training room, and then in the Hartee Visualisation Facility.

CCPi Prizes at ToScA 9-10 September 2013. Our acssociated network CCPi collaborated with the 1st ToScA meeting in the NHM.


Prof Phil Withers presenting 4D Tomography techniques, but also details of iterative and quantification methods.The organisers and CCPi had a tough job awarding prize winners at the poster and art show, and then


relaxed to dine with the locals.


EGUK Chapter Meeting in Bath. 5-6 September 2013

SeiUCCR Using e-Infrastructure for Research Summer School, 27-30 August 2013.



Multiscale presentation, plus a scale corrected version of paraview within the curved wall (photos by Damian Jones, 30/8/13).

A Crew from Horizon Productions visited regarding the 'Daresbury Research Collaboratory': description of the uses within Hartee system and IBM, as well as next systems.



Dr Stefano Rolfo described CFD work that uses Code_Saturne from the BG/Q system: 27/8/13.

Tomo-and-Coffee Sessions at RAL. This is scheduled to hit the Harwell campus in September; likely to be last Friday of each month. Consisting of a short talks/show-and-tells at the AVF (Atlas Visualisation Facility) in RAL along with opportunity to discuss data visualisation with your data.


Dr Mark Basham (Diamond) at a checking session for software suitability on 20 August 2013 - proved connections worked. Announcement of room is open for bookings.

e-Infrastructure Trainers Workshop: image of demonstration from curved wall display (thanks to Mike Croucher, University of Manchester 14 August 2013).


The experimental presentation was to describe six different applications all related, but different in scale, on the same 10.25mx2.3m curved wall; with last one filling the screen.

Visualisation Assistenace for TSB Space Applications Catapult - image pre-production stages for Sky at Night broadcasts in May and August, 2013, on "Stunning Saturn" and "Exploring Mars" episodes.


RAL Atlas Visualisation Facility - new room hand-over with inaugural event on 1st July 2013. Room will be complete with high-end massive memory machines for quantitative visualisation work. This room is now bookable on the STFC calendar.


Summer School (15-19 July, 3013): vis course packs out the visualisation suite.
Overall there was a successful use of the facilities by the invited lecturers and relevant demonstrations were shown at specific points - proof we are able to host 45 plus – as a maximum in the main Crosfield Visualisation room.


Prof David Duke, University of Leeds presenting at the STFC Crosfield Visualisation room (17/7/13)

Manchester CT reconstruction at Diamond workshop - 9th July 2013. 22 attendees

Pop-up training node - 24-26 June 2013, Avizo (VSG) course held at RAL. Course in collaboration with DLS, STFC and RCaH. Software to be installed and made available to appropriate users.


Fabian Arnaud (Applications Engineer, VSG - an FEI company) gave a three day training session in introduction to avizo and various quantitative visualisation techniques.

Hartree Open Day 25th April 2013


Jonathan Smith, Tech-X Ltd Daresbury SciTech, demonstrating VisIT, "Accelerator physics and design studies" (Repeated and updates for IoP Plasma Wakefield Workshop: 18/6/13)

Hartee Centre: BlueRay/DVD filming 8th-12th April 2013 - vis components. DVD to be released soon.


Martyn Wynn - presenting work on CCP4 and related topics



Here are some examples of applications from various other places.

All have credits to sponsors etc including "We acknowledge use of Hartree Centre resources in this work. The STFC Hartree Centre is a research collaboratory in association with IBM providing High Performance Computing platforms funded by the UK's investment in e-Infrastructure. The Centre aims to develop and demonstrate next generation software, optimised to take advantage of the move towards exa-scale computing."

Future Plans and Opportunities to be considered

  • Touchscreen outreach

Based on the setup Sri Nagella was consulted to assit in at the University of Reading. The YouTube? video is here:

For under £200K you have a very large touch-screen that is relatively easy to program and use. Reading (Jon Blower) has this installed since Easter 2014 and has a list of uses etc. (teething problems as well) post honeymon period. As a high-resolution, speedy-response and practical device for analysis and outreach - I would recommend it for certain data sets. Need to consider who would use it and where it could be placed?

Visualisation Facilities (old)

Here is some older information about facilities on the Daresbury Science and Innovation Campus .

Here is some more background information.

  • DCV - Deep Computing VIsualisation, now supported by NICE
  • Visualisation for HPC a Focus Group of the HPC SIG
  • UKHEC technical notes on visualisation and case studies
  • VizNet JISC funded collaboration

Site Tools of the Visualisation Web


  • You are currently in the Visualisation web. The color code for this web is this background, so you know where you are.
  • If you are not familiar with the TWiki collaboration platform, please visit WelcomeGuest first.

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jpgjpg ssmp3.jpg manage 1805.1 K 26 Sep 2013 - 08:54 MartinTurner  
jpgjpg ssmp3_s.jpg manage 42.6 K 26 Sep 2013 - 08:53 MartinTurner  
jpgjpg ssmw2_c.jpg manage 393.1 K 23 Dec 2013 - 09:47 MartinTurner  
jpgjpg ssshowandtelldragonfly_cw.jpg manage 44.3 K 07 Feb 2017 - 09:11 MartinTurner  
jpgjpg stitch9728_9w.jpg manage 15.2 K 24 Jun 2015 - 15:24 MartinTurner  
jpgjpg strip1w.jpg manage 28.7 K 27 Sep 2016 - 09:20 MartinTurner  
jpgjpg strip_sat_c.jpg manage 20.0 K 13 Sep 2013 - 20:24 MartinTurner  
jpgjpg stupost1_w.jpg manage 36.0 K 05 Sep 2014 - 16:32 MartinTurner  
jpgjpg tbdvizmw.jpg manage 31.7 K 28 Jul 2014 - 20:01 MartinTurner  
jpgjpg tcvcrec101014w.jpg manage 37.7 K 13 Oct 2014 - 15:34 MartinTurner  
jpgjpg tn_tncJan-17b.jpg manage 78.6 K 21 Dec 2016 - 09:27 MartinTurner  
jpgjpg tosca0sw.jpg manage 25.5 K 22 Sep 2016 - 15:07 MartinTurner  
gifgif tosca1sw.gif manage 68.4 K 22 Sep 2016 - 14:59 MartinTurner  
jpgjpg tosca2sw.jpg manage 31.9 K 22 Sep 2016 - 14:59 MartinTurner  
jpgjpg tosca3sw.jpg manage 26.3 K 22 Sep 2016 - 14:59 MartinTurner  
jpgjpg tosca_comp_cs.jpg manage 27.7 K 11 Sep 2013 - 22:05 MartinTurner  
jpgjpg tsbskyatn_cs.jpg manage 40.8 K 12 Aug 2013 - 09:08 MartinTurner  
jpgjpg ttpano1w.jpg manage 48.9 K 23 Jun 2015 - 12:00 MartinTurner  
jpgjpg vis2015p12.jpg manage 205.7 K 05 Oct 2015 - 07:55 MartinTurner  
jpgjpg visaatrigi_cw.jpg manage 21.7 K 07 Feb 2017 - 09:14 MartinTurner  
jpgjpg visapsijan2017_w.jpg manage 22.2 K 11 Jan 2017 - 13:04 MartinTurner  
jpgjpg viscourset.jpg manage 27.3 K 23 Jul 2014 - 08:08 MartinTurner  
jpgjpg visimeet1w.jpg manage 18.3 K 13 Aug 2014 - 14:27 MartinTurner  
jpgjpg volummpss_c.jpg manage 80.1 K 14 Oct 2014 - 09:29 MartinTurner  
jpgjpg websccpin.jpg manage 79.0 K 15 Mar 2016 - 15:04 MartinTurner  
jpgjpg websccppetmrn.jpg manage 68.6 K 15 Mar 2016 - 15:04 MartinTurner  
jpgjpg wmgcomp_cw.jpg manage 31.8 K 14 Jul 2017 - 08:45 MartinTurner  
Topic revision: r665 - 26 Sep 2017 - 09:13:23 - MartinTurner
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