Location and RegistrationsAtlas Visualisation Facility: Monday 12 June 2017 - registration at:

• Working Group: https://www.eventbrite.co.uk/e/ccpi-working-group-

meeting-tickets-32227704933

• Fringe meeting: https://www.eventbrite.co.uk/e/roundtable-event-

preadvances-in-x-ray-imaging-tickets-32623491742

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

Agenda CCPi Working Group• Approval of past six months activities (SN)

– approval of secretariat roles http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/CCPSecretariatRole

• Exchanges

– Short presentation on Drishti-Prayog guide (SN/EY) update (MT)

– Fellowships including link and first images from IMAT - ICAL/Brum/Oxford etc (SN)

• addition scan at DLS of BSI 4/4/1 samples

• CCPi have letters of support for fellowship applications;

– EPSRC Manufacturing Fellowship/ EPSRC RSE II x2 / Ser Cymru Fellowship; and a tomiz.org proposal with kitware - to

maintain developers.

• EU COST links and future proposal (19 June 2017) OC-2016-2-21631 'Tomography Across Modalities and Scales'

• Flagship update (DK/JJ)

• Software plan / coding milestones (SN)

• New actions / milestones (SN)

• Web-site

• Future meetings

– dXCT - NPL/BSI @WMG and ToScA @Portsmouth

• Update from 'sister' CCPPETMR network (KT)

• Short Talks:

– Nghio Vo (DLS)

– Srikanth Nagella - CIL (CCPi Core)

• Review mid-term forecast targets

• AOB

Action List from November 2016• 21.11.00 Send any corrections to previous minutes to MT All

• 21.11.01 Visiting fellows suggestions All Ongoing

• Seek e-Science journal for reconstruction work MT/MS Ongoing

• Arrange talks on Savu , IMAT and Avizo frameworks MT Ongoing

• Announce training courses on the CCPi email list MT Ongoing

• Encourage people to add data sets to Zenodo. ALL Ongoing

• Case studies on beam hardening and quantification, RF/SN Ongoing

• Contact NPL to see if they can make use of Zenodo site for their data sets. MT Ongoing

• For high speed files transfers to/from DLS ask local admins to allow firewall bypass. MT/All

• Seek ISIS IMAT data to publish on Zenodo site. SN Ongoing

• GD and BL to discuss editing new Phil Trans issue on reconstruction. GD/BL Ongoing

– Suggest articles for new Phil Trans issue ALL Ongoing

• Arrange visit by Astra developers MB

• Updated proposal for joint CCPi/CCP PET/MR workshop late next year MT/BL/KT Ongoing

• Discuss of policy on CCPi support for attending training courses. PW/MT Ongoing

• Send suggestions and contributions to CCPi report to CCP steering group to MT. ALL

• 21.11.02 Find suitable form of words for acknowledgement for CCPi/EPSRC support and add to website. Also for CCP PET/MR MT/RF

• 21.11.03 Help install Savu on Scarf and UoM machines SN

• Arrange meeting with BL and MB to set objectives for new recruit at STFC. MT/BL.MB/EY

• Request additional codes to include in CCPi quantification software MT

• Contact Brian Bay to see if DVC code can be included CCPi quantification software MT

• Set dates for formal releases of the CCPi quantification software SN

Exchanges

• There have been three European visitor exchanges: 12-13

June 2017 - Andy King, Asa Barber and Margie Olbinado;

• November 2016 at DTI visit; CCPi lunch for four (B. Lionheart)

with Soren Schmidt, Markus Strobl, Morten Sales

• One lab based exchange, Russell Garwood/Imran Rahman

(IMAT-ICAL): 19 May 2017 IMAT/ISIS test tomography;

Manchester Museum artefacts.

Fossil crab (I.

Rahman) –

820A, B, C)

Seminars• 14-15 December 2016 Computing Insight UK 2016 http://www.stfc.ac.uk/ciuk over

250 delegates and suppliers present - Tomo-vis talk given

• 9-12 January 2017 Workshop in Switzerland focused on the visualisation of complex imaging: https://indico.psi.ch/conferenceProgram.py?confId=4840 Reconstruction techniques for 4D data; Multidimensional image processing with special interest on time evolving data; Visualization techniques for multidimensional data; How can the large scale research facility users benefit from advanced analysis and visualization techniques

• 31 January 2017 Software Show-and-Tell 2pm in the RAL Atlas Visualisation Facility: Mark Basham et al., SuRVoS (Super-Region Volume Segmentation) Workbench is a new software for semi-automated segmentation of 3D image volumes. It has been developed jointly between the University of Nottingham, UK and Diamond Light Source, UK and is open source: https://diamondlightsource.github.io/SuRVoS/

• SCD/STFC CCP Seminar, 9 February 2017; 2pm (Room S44 / R89) - Hamish Carr, University of Leeds on 'Contour tree and how it can be used for image analysis -scalability will be discussed for a system that can be tightly coupled with data analysis'

Three exhibitions:

• 4-18 November 2016

Supercomputing Videos and

interactive volume visualisation

system at Hartree Centre stand

#1137:

• Regius Professor in Materials event

for 150 invited guests at

Manchester, April 2017

• Public Engagement: MRI

touchscreen datasets and images

on display at British Science Week

13 March 2017

Training:

• 8 Avizo courses at Manchester (6&7 December 2016; 26 January, 18 April, 19 April, 25 May and 13&14 June 2017)

• CCPi topics course at RAL, 13 December 2016 Analytic Visualisation Features: CCPi Topics - Reading (Diamond nexus) data and scripts to python and quantification algorithms.

• Workshop on SuRVoS (Super-Region Volume Segmentation): high-level algorithms for feature detection, and super-region building for smarter, quicker segmentation and analysis: at Diamond Light Source on May 4-5 2017

• CCPi sponsored an EGU course, 25 April 2017 "3D and 4D imaging: Automation of data analysis" Jose Godinho http://meetingorganizer.copernicus.org/EGU2017/session/25578

BSI Standards involvement:

• 11 January 2017 BSI standards meeting of the

XCT panel (TDW/4/4/1)

• XCT user meeting events@npl.co.uk 8 March

2017

Developers' days:

• Developers' days:20 March 2017 pre-Flagship

meeting at RAL and 11 May 2017 telephone-

conf update.

Papers etc:

• Video usage on CCPi youtube channel in total

is: 8,299

(51+63+67+81+109+251+7109+338+230) and

19 touchscreen examples exist (1x cfd, 10x3d

models, 6xvideos, 2xmri models).

• Data sets on archive: (one on dropbox - needs

moving to zenodo); (new sparse-dataset; and

two new links from Llion Evans)

Continual CCPi support for the three

annual events:1. 13 June 2017 "Advances in X-ray Imaging" Workshop in RAL - CCPi

Sponsored with RCaH https://advances-in-x-ray-imaging-ii.eventbrite.co.uk

2. Dimensional X-ray Computed Tomography Conference, 13 July 2017 at

Warwick http://www2.warwick.ac.uk/fac/sci/wmg/research/pe/ct/events

3. ToScA 2017 (6-8 September) the 5th annual Tomography for Scientific

Advancement symposium addressing hard and soft tissue imaging,

understanding materials in 3D, recent advances in hardware and software,

and a broad range of applications in tomography

www.rms.org.uk/tosca2017

Flagship

update DK/JJ

See separate pdf files.

Including:- IMAT/ISIS test tomography; Manchester

Museum /Brum / Oxford artefacts (SN)

Progress Q4(2016)-Q1(2017) • Mr. Srikanth Nagella

Code Inventory

Beam Hardening

• Working with Matthew Pankhurst et al at

RCaH on paper for Software-X Journal:

– Added new test cases using known materials

– Extended documentation

– Added code to make it easier to pre-process the

crown images

– Included designs for the crown test device

– Software available on CCP Forge server

Preparation for CIL

• CCPi reconstruction code integration with

SAVU

Drishti-Prayog user guide

• This is an updated version of the first version

created by DLS.

• The document is available on CCPi website.

IMAT Experiment with

ICAL/Oxford/Brimingham

IMAT Experiment with

ICAL/Oxford/Brimingham

Software plan / coding milestones (SN)

• …

New actions / milestones (SN)

Current set for 2016-2017 are:

• Website, mailing lists, source code and data archives

• Organise working group meeting and monthly joint show-and-tell sessions

• Support current training courses and organise developer workshop to teach

• Embed framework: ISIS/IMAT

• Embed framework: DLS/savu

• Embed lab based framework: UoM/ UoS/ UoW

• Add quantitative code examples from the community

• Add pre-processing stages inc. beamhardening correction experiments at DLS.

• Organise the main ToScA conference; September 2016

• Optional: Iterative code for the Nikon XTek X-Ray CT accelerated versions (OpenCL, Xeon Phi - KNL)

• Optional: Optimise OpenCL projection algorithms.

CCPi – Collaborative Computational Project in Tomographic Imaging

…aims to provide the UK tomography community with a toolbox of algorithms that increases the quality and level of information that can

be extracted by computer tomography.http://www.ccpi.ac.uk/

Website items

CCP PET-MR…The recent integration of positron emission tomography (PET) and magnetic

resonance (MR) imaging into a single simultaneous imaging system opens up exciting potential for synergistic imaging. This EPSRC-funded collaborative computational

project (CCP) aims to bring together the best of the UK's PET and MR image reconstruction expertise to capitalise on this unique opportunity.

http://www.ccppetmr.ac.uk/

https://zenodo.org/collection/user-ccpi

26

Update from 'sister' CCPPETMR

network (KT)

Two Short Talks:

Nghio Vo (DLS)

- confidential

Srikanth Nagella - CIL (CCPi Core)

Core Imaging Library (CIL)

Mr. Srikanth Nagella

Motivation

Implementation

• Standardising:

• Distribution process: Python via Conda channel

• Documentation: ReadTheDocs

• Release Cycles: 2 times a year. (First release is end of June 2017)

Milestones

• June 2017

• Python releases

• Quantification (4 algorithms)

• Reconstruction (6 algorithms)

• Pre-processing (Beamhardening)

• Segmentation (1 algorithm)

• December 2017

• Release plugins for Avizo, Paraview and ImageJ

• Missing Wedge reconstruction.

• SAVU integration.

Pre-Processing

Beam Hardening

Reconstruction

• Conjugate Gradient method for Least Squares (CGLS)

• Maximum Likelihood Estimation Method (MLEM)

• Simultaneous Iterative Reconstructive Technique (SIRT)

Quantification

• Accessible Volume

• Label quantification

• Particle tracking

Segmentation

• Simpleflex

CCPi python channel

• https://anaconda.org/ccpi

Review mid-term forecast targets

Networking

• User base • 300 members of network • Expand to include neutron tomography

• International links • 3 International Fellows visits

• Links with industry • 5 companies attend our annual conference/year • 10 Industrialists attend training courses/workshops

• Feedback from workshops/training • 100 different people have attended workshops/training

• Outreach • 2 how-to videos/webinars • 5 outreach videos for schools available on youtube • 5 touch-screen 3D models

Software development

• New scientific functionality added • Beta version of our image acquisition and analysis workflow capable of running our tools running on synchrotron data • 3 pre-processing analysis routines added • 4 post-processing analysis routines added • 2 reconstruction tools added for multi-modality

• Ability to run on new platforms • 2 GPU/Phi/FPGA version of codes piloted

• New algorithms • Beyond 3D – multimodal reconstruction • Fewer projection methods • Fully documented iterative algorithm for cluster systems

• Papers • 8

• Complementary funding • 2 parallel funded projects (industry or Research Council)

39 40

Phil Trans Journal Issue #2 and new

IOP Journal (MS)

42

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 beamlineI12. 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 available from Journal page: http://rsta.royalsocietypublishing.org/content/373/2043

AOB

• Summer school in Bath …

• Note: more members of WG acceptable - although should consider

elections if >20

• Need a ‘True’ loop in any future dataflow framework): Joint

reconstruction; Rich tomography;Fast tomography

• Workshops / Connections: Synergistic Workshop with PET-MR Multi-

scale Tomography (CCP5/ CCP-EM ...): emphasis on quantification

AAOB• Project proposal with Drishti (Ajay Limaye) and DLS (Mark Basham) being planned

• Project linking TIGRE with Bill Lionheart’s spiral reconstruction code

• Project MIRAN code with CCPi developers (NE-Scientific - Andrea Borsic)

• Software hacking the Nikon X-ray system (Parmesh Gajjar and Andrew Ramsey)

• Software linking the original Valeriy Titarenko’s reconstruction code to have a CCPi archive

• Royal Society special issue: next one

• New IoP Journal update (~March 2017)– ... and links with ToScA sponsors: RMS

• Workshop: “Quant Across Scales - Link to CCP5 and CCP-EM” (John Purton, Martyn Winn, etc)

• Rich Tomography proposal (Christopher Egen, Bob Cernic, Daniil Kazantsev etc)– ... link to S-J C and MT for sections

• CECAM event at DL – on Drishti / Avizo

Proposals (speculative):

• Link with Newton Fund (Global Challenge Research Fund) regarding STFC activities

• Speculative with Innovate UK – Bill Lionheart

• 3DSIM Inc – additive manufacturing contact (mathematical simulation)

• Links with CFD groups – links and discussion with groups in UoM and STFC.

Datasets:

• QMUL dataset x2

• Upload a public space for touchscreen demonstrators

• MSc project (at UoM)

• EPSRC case studies as per previous WG minutes

• New CCPi poster requested

• Logos on stickers and mugs– Badges NOT FBP

• STFC PE grant for "Fornesic CSI" on tomography... including ISIS users.

Emails:

Srikanth Nagella (srikanth.nagella@stfc.ac.uk),

Erica Yang (erica.yang@stfc.ac.uk),

Edoardo Pasca (edoardo.pasca@stfc.ac.uk),

Ron Fowler (ronald.fowler@stfc.ac.uk),

Evgueni Ovtchinnikov (evgueni.ovtchinnikov@stfc.ac.uk)

Martin Turner (martin.turner@stfc.ac.uk) (martin.turner@manchester.ac.uk)

Barry Searle (barry.searle@stfc.ac.uk)

Flagship CCPi:

Daniil Kazantsev (daniil.kazantsev@manchester.ac.uk)

Jakob Jorgensen (jakob.jorgensen@manchester.ac.uk)

CCPi is at: http://www.ccpi.ac.uk/

CCP PET-MR is at: http://www.ccppetmr.ac.uk/

Floagship link: http://www.ccpi.ac.uk/node/275

See NEWS section at:

http://tinyurl.com/STFCVis

47

To run the network the following roles are undertaken:

• Publish and edit a "weekly" Joint Email Newsletter (email both ccpi-petmr@jiscmail.ac.uk and ccpi-members@jiscmail.ac.uk)

• Events diary update – on a combined drupal site https://www.ccpi.ac.uk/node/events

• Update other meeting pages on drupal items http://www.ccpi.ac.uk/ and http://www.ccppetmr.ac.uk/

• Twiki update for events with photos for all items http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/WebHome#News

• Email list management JISCMAIL etc (full list): these currently include adding and emailing new attendees:

– CCP-PETMR CCP-PETMR-DEVEL, CCP-PETMR-USERS CCPI-MEMBERS

• Business hosting sessions have been approximately monthly - software show-and-tell events and other items: involving invitation/hosting/contacts etc

Update wiki and keep numbers etc: http://tinyurl.com/STFCVisSem

• CCPi and CCP PETMR conferences: eg ToScA liaison and fund raising

• Drupal website page editing and newsflash additions: http://www.ccppetmr.ac.uk/ and https://www.ccpi.ac.uk/

Booking, reports, editing and minutes for the following formal management meetings need coordinate. Using eventbrite, email and websites etc..:

• CCPi Working Group - every 6 months CCPPETMR Working Group - every 6 months

• CCP Steering Panel representation as needed - every 6 months CCPi exec meeting – every 6 months

• CCP PETMR exec meeting representation - bi-monthly SLA SP representation when required (annual)

• PETMR software development meetings (every 6 weeks) and weekly t-conf meetings

• CCPi developer meetings – tour of lab based sites included (every 3 months)

• Monthly? meeting for show-and-tell and other CCP related activities (eg SCD seminars advertised to the wider community)

• Coordinate EPSRC mid term and final reports (every two years) with Damian and Barbara

For all these deliverables and other data - Data/Docs:

• Update PETMR onedrive account and shared files folder on drupal including admin folder (lists etc)

• Update CCPi shared files folder on drupal as well as dropbox links and zenodo accounts for datasets

There are other criteria that have played a large role - mainly EPSRC deliverables for main network:

• PE activities; many events have occurred and thousands of public have been through specific vis CCPi/CCPPETMR demonstrations: attend

• Create new CCP outcomes for example on KTA exhibition stands/ conference stands etc

• Liaise with CoIs and network members for future Proposal Planning etc. new networks

Both involve fellowships and small grants this involves:

• Arranging travel and expenses as needed Approval and summary reports

• Hosting and travel with fellows to visit sites and guide

Occasional visits for funded external trips and representations have been requested including

• EU COST EXTREMA visits and meetings PSI visits and workshops

• BSI conferences (including work/visits with NPL)