location and registrations agenda ccpi working...
TRANSCRIPT
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 [email protected] 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 ([email protected]),
Erica Yang ([email protected]),
Edoardo Pasca ([email protected]),
Ron Fowler ([email protected]),
Evgueni Ovtchinnikov ([email protected])
Martin Turner ([email protected]) ([email protected])
Barry Searle ([email protected])
Flagship CCPi:
Daniil Kazantsev ([email protected])
Jakob Jorgensen ([email protected])
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 [email protected] and [email protected])
• 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)