Past and present seminar information including links for visualisation.

Seminars and vis sessions (http://tinyurl.com/STFCVisSem) across the sites.

Tomo-and-Coffee Session: 3D Volume Data Visualisation: Software show-and-tell. Atlas Building - Atlas Visualisation Facility. Scheduled in the Atlas Building at the Harwell campus during sometimes the last Friday of each month from 2pm we have open sessions. Consisting of a short talks/show-and-tells along with opportunity to discuss visualisation needs with your data.

Lunch and Learn sessions at Manchester MXIF at 12non with pizza

Directions: Google Maps to the Atlas Visualisation Facility: https://mapsengine.google.com/map/edit?mid=zkkpP5ii84bY.krIHgGkZaXa4


Lunch-and-Learn Sessions; often at 12 noon - second Tuesday of the Month in Manchester

Proposals for 2018-2019 from October 2018:

  • new CCPi Flagship results
  • ATI project Wilfrid Kendall and Julia Brettschneider (Warwick)
  • ML seminars from students at RAL
  • ENGINX
  • ...

Schedule:

  • 9 July 2019
  • 11 June 2019 clash with Fringe
  • 14 May 2019
  • 9 April 2019
  • 12 March 2019
  • 12 February 2019 (provisional) Beatriz Mingo Suggested session on coatings (thermal, barrier, oxidation and corrosion resistant) Also invite wider coatings community to talk
  • 15 January 2019 (provisional) Sarah Fisher and Parmesh Gajjatr - laminography
  • 11 December 2018 Experience from two Summer students on ML and Nghai Vo "Tomographic data for testing, demonstrating, and developing methods of removing ring artifacts" and "Python implementation of distortion correction methods for X-ray tomography" - https://zenodo.org/communities/ccpi
  • 13 November 2018 ToScA (and other events); Chakri Gudla "Multiscale correlative characterization of environmentally assisted crack initiation, propagation and failure in a high strength aa5083 h131 alloy" and Sam Johnston "Non destructive 3D grain imaging in aeroengine materials by diffraction contrast tomography"
  • 2 October 2018 Brian Bay "DVC" and Daniil Kazantzev "Tomophantom package" - at RAL v-conf to Manchester (att 28+6)
  • 10 July 2018 ICAL Russell Garwood ; and new (scalable) reconstruction package from the MTC Nick Brierley (att 22)
  • 12 June 2018 Jakob Jorgensen and Parmesh Gajjar "Advancing automated temporal-CT capabilities of laboratory μXCT machines" (att 11)
  • 8 May 2018 Wenjuan Sun and Stephen Brown NPL; Title: Recent development in dimensional X-ray computed tomography at NPL for advanced manufacturing (att 19)
  • 10 April 2018 - Genoveva Burca, Instrument Scientist - IMAT, ISIS Facility "IMAT- neutron imaging and diffraction instrument for materials science at the ISIS neutron spallation source" (att 21)
  • 13 March 2018 - Catherine Disney Microstructure and Mechanics of Intervertebral Discs from Phase Contrast Synchrotron X-ray Tomography (att 20)
  • 13 February 2018 - Yi Guo “Characterizing voids during ductile fracture of a dual phase steel using X-ray computed tomography and serial sectioning EBSD” and Shelley Rawson “Bio and bio-inspired materials” (att 27)
  • 16 January 2018 - Adam Cooper X-ray tomographic analysis and characterization of ductile damage, William Brayshaw Ductile fracture behaviour of Reactor Pressure Vessel steels (att 20)
  • 13 December 2017 - CIL CCPi Sri Nagella (att 19)
  • 7 November 2017 - Nick Curry An Investigation into Rust Layer Microstructure (att 30)
  • 13 September 2017 - Alistair Garner Advanced 3D characterisation of iodine-induced stress corrosion cracks in zirconium alloys Jose Godhino BP summer placements (att 22)
  • 9 August 2017 - Nghai Vo "Developments of image processing techniques for tomographic data at synchrotron facilities" from Diamond Light Source; Martin Turner on dXCT activities (att 22)
  • 19 October 2016 - review at Manchester on ToScA
  • 18 May 2016 - inc a follow on Training Session with Parmesh Gajjar on hacking the Nikon imaging devices (initially the custom bay units).
  • 16 March 2016 - Michael McCarthy (NPL), University of Manchester HMXIF, "Industrial XCT: Current develops of a dimensional verification standard for XCT (ISO 10360)”
  • 1 May 2015 - Bill Lionheart will talk about Fast Tomography: From Airport Baggage Scanning to Materials Science.
  • 27 February 2015 - Martin Turner “Visualisation Matters - the need to put the human back in the imaging-capture-and-computational loop: case studies from work with the CCPi (http://www.ccpi.ac.uk/) and Harwell Imaging Partnership as well as future opportunities for collaboration and resource"


SCD based Seminars:

17 May 2018, 10am-12noon Avizo hands-on session with FEI at RAL. Introductory to Avizo software, pipeline and then running a simple segmentation and video production.


SCD Seminars: Raymond Chan, from the Chinese University of Hong Kong 2 November 2017: http://www.math.cuhk.edu.hk/~rchan/ and Jim Nagy, from Emory University in the USA ( 7 December 2017): http://www.mathcs.emory.edu/~nagy/ 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": https://www.newton.ac.uk/event/vmv


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 (robert.atwood@diamond.ac.uk). 2 October 2017, 2pm


SCD Seminar at 2pm, 11 September 2017: https://www.ccpi.ac.uk/node/306 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.


CCPi Flagship Meeting 2pm-4pm - open sessions from 3pm at RAL; 20 March 2017


CCP Seminar, 9 February 2017 - 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 t ightly coupled with data analysis' 2pm Held at RAL and via Video Conference.


2:00pm-3:00pm: Monday 31 January 2017 - Software Show-and-Tell 2pm in the RAL Atlas Visualisation Facility: Mark Basham, Imano Luengo, Michele Darrow 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/ RAL AVF (Atlas Visualisation Facility) and VC available - local host Sri Nagella.

Video Streamed to PSI Seminar Room (3.306, Alan Turing building) at University of Manchester - local host martin.turner@manchester.ac.uk

tn_tncJan-17b.jpg Abstract; "SuRVoS brings together machine learning models, computer vision techniques and human knowledge within a user interface to interactively segment large 3D volumes. The user interface of SuRVoS is divided in two panels. One panel contains all the available plugins (or tools) and the other panel, instead, resides the visualisation panel (where everything made with SuRVoS will be visualised) and another two main workflows. SuRVoS is able to work with very large datasets by means of its Region Of Interest (ROI) system and a HDF5 workspace. Everything loaded with SuRVoS and every action made within it will be saved in a workspace folder inside an HDF5 file. HDF5 is an on-disk data format that loads only the required data on memory. By using ROIs, SuRVoS limits all its actions to the selected ROI, which allows the user to load large datasets but operate only in small windows, also improving the performance of all the subsequent actions."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/ imanol.luengo@nottingham.ac.uk


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, srikanth.nagella@stfc.ac.uk Based upon the previous visit by FEI (12 attendance)


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 Mancini Elettra-Sincrotrone Trieste S.C.p.A., 34149 Basovizza (Trieste), Italy beamline scientists of the SYRMEP beamline at the Elettra synchrotron light source.

This has been made available as a podcast.

Abstract: Imaging techniques play an important role in several research fields: medicine, biology, material science, geosciences and archaeology. Optical and scanning electron microscopy techniques are widely adopted tools for the investigation of the texture and morphology in a large range of materials. Imaging techniques based on hard X-ray are also of particular interest and microradiography has proved to be useful for clinical diagnostics and for the investigation of crystal growth.

In recent years great interest has been posed on X-ray computed microtomography (microCT) techniques, employing microfocus and synchrotron radiation sources. These techniques produce three-dimensional (3D) or 4D (dynamic microCT) images of the internal structure of objects with a spatial resolution at the micron- and submicron- scale. Investigations performed directly in the 3D domain overcome the limitations of stereological methods usually applied to microscopy-based analyses and a non-destructive approach is more suitable for further complementary analyses and for precious or unique samples (fossils and archeological finds, in-vivo and in-situ imaging, etc …).

An intriguing challenge is to extract directly from 3D and 4D images quantitative parameters related to the physical properties of the studied materials. Porosity and specific surface area as well as anisotropy, connectivity and tortuosity are interesting descriptors of a 3D model. However, accurate image processing and analysis methods for an effective assessment of these parameters are still an open issue in several applications.

Several scientific applications of advanced hard X-ray imaging techniques will be presented in this seminar, focusing our attention in the field of geomaterials. Examples of results obtained from the 3D morphological and textural characterization of crystals and pores in volcanic products, reservoir rocks as well as cement-based materials will be illustrated.


4:00pm-5:00pm: Friday 12 September 2016 - Novitom http://www.novitom.com/en/ RAL AVF (Atlas Visualisation Facility) and VC (Cisco Jabber) to Whitworth Room in DL - local host Sri Nagella.

tn_tncSep-16b.jpg Novitom is an independent company, specialized in microanalysis, 3D materials characterization and non-destructive testing, based on advanced imaging techniques including synchrotron-powered technology. Novitom also develops customized algorithms for automated analysis of your 2D or 3D images. On demand, Novitom also designs mechanical press or thermal cells compatible with your laboratory imaging equipment. AVF (RAL) and video-link to the University of Manchester. http://www.novitom.com/en/


Twelve Tomography Seminars for the Season 2015-2016 all in one picture:

semseason2015_2016.jpg


2:00pm-3:00pm 8 September and 3pm-4pm 12 September 2016 - From ToScA abstract: Marcus D. Hanwell, S. Waldon, Y. Jiang, C. Quammen, E. Padgett, DA. Muller, R. Hovden - Tomviz: Open Source, Scalable Platform for Reproducible Materials Tomography - local host Sri Nagella.

tn_tncSep-16.jpg Materials tomography using transmission electron microscopy (TEM) involves a number of steps to go from projection images taken on the microscope to an aligned, reconstructed 3D volume. The Tomviz project builds upon a number of open source frameworks to deliver a powerful desktop application for research, leveraging the Python environment along with a number of scientific Python modules to deliver a comprehensive solution for materials tomography at nanoscale to atomic resolution. The development of the application will be discussed, along with the Pythonbased data processing pipeline, and the XML format used to enable complex, reproducible data processing and visualization pipelines. The application is based on Qt, VTK, ParaView, and ITK with a bundled Python distribution making use of NumPy, SciPy, and Python wrapped ITK/ParaView to offer a powerful visualization and data analysis application. The development, packaging, and deployment of a robust, crossplatform application for materials tomography will be discussed. The current state of reproducible analysis and data processing pipelines demonstrated, and future directions will be discussed. The use of Python will be demonstrated within this context. Reproducibility is a key problem in science, and complex data collection, alignment, reconstruction, and processing pipeline are particularly important. This project is funded by the DOE SBIR program, and is an active collaboration between developers at Kitware and scientists at Cornell University. AVF (RAL) and then at University of Manchester.


2:00pm-3:00pm: Friday 12 August 2016 - Ander Biguri and Manuch Soleimani, University of Bath https://github.com/CERN/TIGRE RAL AVF (Atlas Visualisation Facility) and VC (Cisco Jabber) to Whitworth Room in DL - local host Sri Nagella.

tn_tncAug-16.jpg Ander Biguri and Manuch Soleimani, University of Bath Tomographic Iterative GPU-based Reconstruction (TIGRE) Toolbox is a MATLAB/CUDA toolbox for fast and accurate 3D X-ray image reconstruction. One of the key features is the implementation of a wide variety of iterative algorithms as well as FDK, including a range of algorithms in the SART family, the Krylov subspace family, statistical inversion and a range of methods using total variation regularization. Additionally, the toolbox has GPU-accelerated projection and back projection using the latest techniques and it has a modular design that facilitates the implementation of new algorithms. The TIGRE Toolbox is released under an open source license, encouraging people to contribute. AVF (RAL) and video-link to Whitworth, Daresbury Labs.

Eventbrite link: https://www.eventbrite.co.uk/e/ccpi-software-show-and-tell-tickets-26623599904


2:00pm-3:30pm: Friday 11 August 2016 CCPi Interactive Vis - Show-and-Tell http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/ProjectsTouchTable RAL AVF (Atlas Visualisation Facility), and VC (Cisco Jabber) to Whitworth Room in DL - local host Sri Nagella.

tn_tncAug-16p.jpg A meet and discuss for future funds/ fellowships and importantly how to use the Atlas Visualisation Facility at RAL for further Public Engagement activities. The emphasis is on XCT data sets, but other items will be discussed. Items: 1. New version of Drishti/Prayog software - for stereo wall setup; 2. Ideas on how to make sure demos are usable; 3. Discuss the University of Manchester Kiosks; 4. Consider STFC PE grants to create new demos and exhibitions Information at; http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/ProjectsTouchTable AVF (RAL) and video-link to Whitworth, Daresbury Labs.

Eventbrite link: https://www.eventbrite.co.uk/e/ccpi-interactive-vis-show-and-tell-tickets-26624124473


14 July 2016, 11:00am at DL SCD Seminar, Hamish Carr (University of Leeds), "Topological Analysis and Visualisation" Over the past two decades, data generated either numerically or empirically has grown ever larger, while the human ability to process data has not. As a result, comprehension depends more and more on data analysis as a means of supporting (or supplanting) visualisation. One of the principal methods of exploiting analysis has been through the application of the mathematical discipline of topology, which studies invariant properties of functions. In practice, however, mathematics alone are not sufficient, and a significant effort has been required in computational algorithms for topological analysis, in building scalable software to implement them, in constructing user interfaces that take advantage of them, and in validating them by application to real world visualisation problems. In addition to this, however, these methods have also driven deeper understanding of the mathematical relationships between mathematical, computational and visual representations, and have thus uncovered hitherto unsuspected methods for visualising relationships between properties in numerical simulations. This talk will therefore concentrate on an overview of developments in the application of computational topology to visualisation and analysis tasks, but will also examine how the mathematics underlying these methods have also driven developments in non-topological visualisation


6 July 2016, 2:00pm-3:00pm at RAL AND 11 July 2016 at DL SCD Seminar: Dave Pugmire (Oak Ridge National Laboratory), "Visualization and Analysis Services for Extreme Scale Supercomputers" The scientific data that are being generated today, and in the near future, will quickly outpace our ability to process and understand it. The data generated are growing in multiple ways, including the size of the data, the rate at which it arrives, and the varying types of data. Additionally, data are available from multiple sources, including for example, computational simulations and sensor data extracted from experiments. In such situations, workflows for the movement and management of data, as well as the analysis and visualization while the data are in transit, become even more critical, and increasingly challenging. At the same time, revolutionary changes are emerging in the architectures of supercomputers. These changes include tremendous increases in concurrency on each node, as well as a deep hierarchy of memory. These architectures are a challenge for currently running HPC codes, as well as visualization and analysis algorithms. We are, along with collaborators at other national laboratories, and universities, researching and developing a cohesive framework that will enable scientists to manage the growing data problem, and to enable them to extract knowledge and insight. Central to this work is a “Service Oriented Architectures” (SOA) framework that provides a clear separation from the data producers and consumers. Our framework is based on the ADIOS middleware layer, that manages the data as they are produced, and orchestrates movement through the deep memory hierarchy. The data consumers, in this case visualization and analysis services built from tools like VisIt, ParaView, VTK-m, and pbdR, will interact with the middleware layer for access to data, and for coordination to optimize access across the deep memory hierarchy. These services, which will be self-consistent, interoperable operations will enable scientists to construct multiple complex workflows. This talk will present the preliminary research on the development of this framework and the associated services as well as the initial results obtained working with several large-scale simulation codes running on the Titan supercomputer at ORNL. And finally, a detailed discussion on the future research plans and directions that will enable scientific insight on exascale computing systems.


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

Fringe Meeting - 9 June 2016 Collaborative Future X-Ray Roundtable


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


2:00pm-3:00pm: Wednesday 13 January 2016 - Jakob Sauer Jørgensen, Technical University of Denmark "How few projections are enough? Predicting performance of sparsity regularization in X-ray tomography" S44 at R89 (RAL) and video-link to Arkwright, Daresbury Labs Local hosts Daniil Kazantsev sand Sri Nagella.

tn_tncJan-16.jpg Jakob Sauer Jørgensen, Technical University of Denmark How few projections are enough? Predicting performance of sparsity regularization in X-ray tomography Sparsity regularization in X-ray tomography has shown large promise for accurate reconstruction from reduced data, potentially leading to substantially reduced patient X-ray exposure in medical imaging and shorter scan times in materials science. Compressed sensing (CS) has motivated these developments by offering guarantees of accurate reconstruction of sparse images from reduced data under suitable assumptions on the sampling matrix. However, existing CS guarantees, e.g., based on the restricted isometry property (RIP), do not apply to structured and sparse sampling matrices in X-ray tomography. The empirical success of sparsity regulaization in X-ray tomography therefore remains theoretically unexplained. In this seminar I will describe our attempts of establishing a connection between image sparsity and the amount of undersampling admitted by sparsity-regularized reconstruction methods. In particular, I will describe simulation results suggesting how one may predict the sufficient number of projections to acquire based on the sparsity level of the scanned object. I will then describe preliminary results of validation with real data using the SophiaBeads data set recently released from the University of Manchester. S44 at R89 (RAL) and video-link to Arkwright, Daresbury Labs.



3:00pm-4:30pm: Monday 14 December 2015 - "“Bring/Discuss-Your-Own-Data" and see Virtual Reality visualisation" RAL Atlas Visualisation Facility

tn_tncDec-15.jpg “Bring/Discuss-Your-Own-Data" and see Virtual Reality visualisation at the RAL Atlas Visualisation Facility Also launch of the new CCPi website: www.ccpi.ac.uk/ With new license servers being negotiated we are looking again at the Avizo VR toolkit: https://twitter.com/CeriBrenner/status/591602828579332096 Opportunity to explore your data interactively in 3D. Contact srikanth.nagella@stfc.ac.uk to discuss data transfer prior to the event or just turn up to see and discuss.


10:30am-12noon: Friday 26 November 2015 - "Not yet becoming IronMan – but software for Touchable Scientific Visualisations" Martin Turner, Interactive Visualisation Group RAL Atlas Visualisation Facility

tn_tncNov-15.jpg Not yet becoming IronMan – but software for Touchable Scientific Visualisations Martin Turner, Interactive Visualisation Group RAL Atlas Visualisation Facility IVG (Interactive Visualisation Group), update meeting "…to create Touchable Pathways to Impact (and supported initially within the CCPi)" With high-end vis you can (almost) become Ironman (tweet from Laser’s experiment in RAL: https://twitter.com/CeriBrenner/status/591602828579332096) 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 Drishti-Prayog system has been chosen, modified and tested at a range of big events; and includes the first purpose built kiosk. This will be in the AVF – but we will attempt BlueJeans Video Conferencing – please email if wish to attend remotely (martin.turner@stfc.ac.uk)


2pm-3pm: Friday 30 October 2015 - Antoniu Pop Programming and Optimizing Task Data-Flow Applications with OpenStream and Aftermath Local host for this event is Sri Nagella (srikanth.nagella@stfc.ac.uk)

tn_tncOct-15.jpg Antoniu Pop 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.


2pm-3pm: Friday 19 October 2015 - Video Conferencing Mike Groeber Presentation on the general overview of DREAM.3D" http://dream3d.bluequartz.net/?p=1313

tn_tncOct-15b.jpg Mike Groeber, US Air Force Overview of DREAM.3D “Analysing Data with Ease” [6.2.0 Released] DREAM.3d http://dream3d.bluequartz.net/ 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.


Twelve Tomography Seminars for the Season 2014-2015 all in one picture:

semseason2014_2015.jpgsechalf2015.jpg

Update on High Powered Lasers exploitation: August 2015


2pm: 2 September 2015 tn_tncSep-15b.jpg The University of Manchester welcomes researchers at all levels to the CCPi imaging workshops where delegates will gain insights from and engage in troubleshooting sessions with specialists in Drishti/Prayog and Avizo. Held at the Photon Science Institute, home to the Henry Mosely X-Ray Imaging Facility (immediately prior to the Tomography for Scientific Advancement Symposium on 3rd-4th September). 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; https://github.com/AjayLimaye/drishti/releases) 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. (http://www.avizo3d.com) 2 September 2015 4pm-5pm IVG (Interactive Visualisation Group), update meeting. Places are limited and allocated on a first come, first serve basis. To book your place please e-mail your name, institution and any dietary requirements to kate.a.meade@manchester.ac.uk Open Day events on 8-11 July 2015 tn_tncJul-15.jpg Schools Visit day; 95 school visitor came to explore the history of computing and 3D space on the visualisation wall. Main public day on 11 July, with over 15000 visitors; and ~560 saw fluid flow and molecular visualisation presentations.Local host for this event is Sri Nagella (srikanth.nagella@stfc.ac.uk) and Ron Fowler (ronald.fowler@stfc.ac.uk)


2pm-3pm: Friday 24 April 2015 tn_tncApr-15.jpg The Avizo VR Module enables advanced data visualization and analysis with large tiled displays as well as immersive VR configurations like CAVEs. With its unique set of features this Option represents Virtual Reality ready application for scientific and medical visualization in immersive environments. This provides; Full immersive 3D interaction; Support for single and multiple screens; Support for single and multi-pipe and for graphic clusters; Flexible customization for specific display geometry; Head-tracking and tracked hand-held 3D input devices; Control functionality via user interface; and Control of 2D user interfaces with 3D devices (virtual mouse).Local host for this event is Sri Nagella (srikanth.nagella@stfc.ac.uk) 2pm-3pm: Friday 27 March 2015 tn_tncMar-15b.jpg "Noctylio: advanced image analysis software" Sarah Dubreucq, Benoit Recur, Eric Dehez (Noctylio SAS http://www.noctylio.com/) Noctylab v1.0 is a 3D imaging software including a large range of up-to-date image and signal processing algorithms as standards, different 3D visualisation modes such as surface and volume rendering, as well as image and signal analysis, measures and quantification tools. Noctylab v1.0 handles processing sequences that can be created, optimized and thus launched on large datasets in order to maximize computing resource usage and minimize user interactions. Specifically, we will show how Noctylab v1.0 implements tubular shape analysis sequence (archeo-bronchial tree or vascularity) based on 3D skeletonization and topology, in order to get caliber measures along branches. Moreover, the software adaptability allows the exploitation of all these tools from new imaging modalities, such as THz scanners. We will also introduce tools dedicated to hyper-spectral analysis and adapted to time-domain spectroscopy or 3D THz imaging. Such tools aim at combining both image and signal processing techniques to obtain 3D visualisation and benefit from image-based measures/analysis tools from hyper-spectral signals.


3pm-3:30pm: Friday 27 February 2014. tn_tncFeb-15.jpg 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. 3:30pm-4pm: Friday 27 February 2015 tn_tncFeb-15b.jpg IMAT is the first neutron imaging instrument at ISIS. It will also be the first of its kind in the world offering unique time-of-flight tomography-driven diffraction techniques. This project aims to enable novel experimental science capabilities for IMAT through developing and deploying HPC based infrastructure needed for in-experiment tomographic image reconstruction, rendering, and interactions. It will also build the foundation needed to enable energy selective image processing, data fitting and 3D tomography driven diffraction data scrutiny capabilities for IMAT. Details at: http://stfc.ac.uk/SCD/research/data/44593.aspx


2pm-3pm: Friday 19 December 2014 - Talk by Prof Jonathan Blackledge, South Africa. (No Video Conference) From the University of Manchester in the ICAM

Fireside chat on noise/speckle and physics within imaging problems.


2pm-3pm: Thursday 18 December 2014. tn_tncDec-14b2.jpg "Data and Visualisation Needs Survey" Through the EPSRC SLA and via the University of Manchester we have been asked to coordinate some visualisation surveys across certain disciplines. This is to inform current uses as well as indicate trends and developments for future collaboration and high impact visualisation uses. The main surveys completed at the end of October 2014, and are currently being evaluated for long term embedding into a visualisation service. This will be at 2pm at Rutherford Appleton Laboratory on the Harwell Campus: in R89/Access Grid and room A1 in DL from 2pm https://eventbooking.stfc.ac.uk/news-events/3d-volume-data-visualisation-dec14b 2pm-3pm: Friday 12 December 2014 tn_tncDec-14.jpg Talk by Prof Sarah Hainsworth, University of Leicester "Micro-computed X-ray tomography for forensic applications" Micro-computed X-ray tomography allows the 3D visualisation of structures with higher resolution than traditional computed tomography used in medical applications. This talk will show how micro-computed tomography has been used in a number of forensic applications including tool marks in dismemberment, determining the structural development of blow flies and imaging a 500 year old King, namely Richard III. This will be at 2pm at Rutherford Appleton Laboratory on the Harwell Campus: in the RC@H "Research Complex at Harwell" from 2pm. https://eventbooking.stfc.ac.uk/news-events/3d-volume-data-visualisation-dec14 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.


3pm-4pm: Wednesday 26 November 2014. tn_tncNov-14.jpg Sam Worthington (Worthington Sharpe Ltd.) Title "Wing: Beyond the mouse". At Daresbury Labs (STFC) A1 Rylands "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. This will be at 3pm in A1 Rylands Room at Daresbury Laboratory. http://www.worthingtonsharpe.com/index.html wing@worthingtonsharpe.com 3pm-4pm: Friday 10 October 2014 tn_tncOct-14b3.jpg - Talk by Russell Garwood* *Seminar @RAL in R89/S44 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.“ Atlas Building – This will be at 3pm in the Atlas Visualisation Facility that can be found in the Atlas Building at Rutherford Appleton Laboratory on the Harwell Campus. https://eventbooking.stfc.ac.uk/news-events/3d-volume-data-visualisation-oct14


3pm-4pm Friday 26th September 2014 tn_tncSep-14bb.jpg "Image-based simulation of diffusion and flows within experimental volumetric data sets Dr Marcus Campbell Bannerman, University of Aberdeen" Seminar in R89/S44 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 (http://dynamomd.org) 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. 10am-3pm Monday 8th September 2014 tn_tncSep-14.jpg "Drishti 2.5 Workshop" Drishti 2.5 has just been 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. (http://sf.anu.edu.au/Vizlab/drishti/) Latest Code: https://github.com/AjayLimaye/drishti Email Sri (srikanth.nagella@stfc.ac.uk) or Loic (loic.courtois@manchester.ac.uk) to book a spot - being held in RAL, please email as limited space. Schedule: 9am- Coffee/tea 10am-short workshop on Drishti 12:30 Lunch and tours (Loic Courtois) 2pm-4pm Discuss vis data issues


Twelve Tomography Seminars for the Season 2013-2014 all in one picture:

semseason2013_2014.jpg


2pm-4pm Friday 1st August 2014 tn_tncAug-14b.jpg "Bring Your Own Data Day II" Do you have volume image data you'd like to analyse? Or do you have an analysis method that you want to make more efficient? If so, come along to the CCPi Bring Your Data day at the Atlas Visualisation Facility at RAL on Aug 1st from 2pm. We will provide help with image analysis using Avizo and Avizo Fire whether it's image registration, thresholding, segmentation or extracting data from the image. We can also talk about scripting the calculations and even creating custom modules to implement your algorithms using C++ and ITK where appropriate. We will have a large memory machine (1/2TB) available if you have a large amount of data. We can also display laptops on the big screen if you wish to keep data on your own machine - The meeting will start at 2pm in the Atlas Visualisation Facility. This can be found in the Atlas Building at Rutherford Appleton Laboratory on the Harwell Campus. https://eventbooking.stfc.ac.uk/news-events/3d-volume-data-visualisation-Aug14


2pm, Thursday 26th June 2014 tn_tncJun-14.jpg Welcome to the Data Analysis WorkbeNch. Data Analysis WorkbeNch (DAWN) is an eclipse based workbench for doing scientific data analysis. It implements sophisticated support for : (1) Visualization of data in 1D, 2D and 3D (2) Python script development, debugging and execution and (3) Workflows for analyzing scientific data calling Python and binary codes. DAWN is not restricted to one scientific domain. It is developed by and for the synchrotron community foremost but has strong overlap with other communities like neutron scattering, photon science and any scientific communities with the above or similar needs: http://www.dawnsci.org/ The meeting will start at 2pm in the Atlas Visualisation Facility. This can be found in the Atlas Building at Rutherford Appleton Laboratory on the Harwell Campus. https://eventbooking.stfc.ac.uk/news-events/3d-volume-data-visualisation-jun14 2pm Friday 30th May 2014 tn_tncMay-14.jpg "Paraview Volume Visualisation" ParaView has improved its volume visualiser quiet drastically in the last year. We will informally consider this product over an informal discussion - and show volume vis on the large Atlas Visualisation Facility. (http://www.youtube.com/watch?v=UwKFg0yOlCA). Comparisons with Drishti and Avizo's offerings will be presented. Thoughts on new devices; including touchtables and large touch screens will be presented. The meeting will start at 3pm in the Atlas Visualisation Facility. This can be found in the Atlas Building at Rutherford Appleton Laboratory on the Harwell Campus. 2pm-3pm Pre-Coffee in Electron Building (next door) - TSB Space Applications Catapult Centre No booking required - but welcome to email for detailed logistics: martin.turner@stfc.ac.uk

9:30am, Thursday 8th May 2014 tn_tncMayA-14.jpg Avizo 8.1 has just been released in April 2014, and on Thursday 8 May, Joseph Baptista and Fabien Arnaud from VSG/FEI will be giving a short workshop in RAL. For Materials Science users there are two main features; improved FFT, Porosity calculations and also direct links to FEI imaging machines. http://www.vsg3d.com/sites/default/files/WhatsNewAvizo81.pdf Email Sri (srikanth.nagella@stfc.ac.uk) to book a spot - being held in RAL, please email as limited space. 3pm, Friday 28th March 2014 tn_tncMar-14.jpg Digital Volume Correlation (DVC) from LaVision - a novel tool for quantifying full-field displacement and strains" Abstract: Dave Hollis from LaVision will be discussing DVC. Digital Volume Correlation (DVC) is a novel tool for quantifying full-field displacement and strains throughout material volumes having undergone deformation. The technique is an extension of 2D digital image correlation and uses the conservation of gray-scale levels of 3D volumes obtained using a volume imaging technique such as X-ray CT. The material’s natural or artificially introduced internal pattern is tracked between subsequent volumes allowing the investigator to truly understand the subsurface material behaviour and validate complex simulations. In this meeting Dave Hollis from LaVision (dhollis at lavision.com) will give an overview of the technique and show some of the results possible. Also present will be Faye Gillard of The University of Southampton muVis centre, and has experience of applying DVC to a variety of materials and test cases. Faye is a Knowledge Transfer Secondee (KTS) working with muvis and LaVision to further develop the technique by exploring new materials and applications. There will be ample opportunity to discuss DVC with Dave and Faye during this meeting. The meeting will start at 3pm in the Atlas Visualisation Facility. This can be found in the Atlas Building at Rutherford Appleton Laboratory on the Harwell Campus. https://eventbooking.stfc.ac.uk/news-events/3d-volume-data-visualisation-mar14

3pm, Friday 28th February 2014 tn_tncFeb-14.jpg Jon Taylor (ISIS): The Mantid project provides a framework that supports high-performance computing and visualisation of scientific data. Mantid has been created to manipulate and analyse Neutron and Muon scattering data, but could be applied to many other techniques. The framework is open source and supported on multiple target platforms (Windows, Linux, Mac). (http://www.mantidproject.org/Main_Page) The meeting will start at 3pm in the Atlas Visualisation Facility. This can be found in the Atlas Building at Rutherford Appleton Laboratory on the Harwell Campus. https://eventbooking.stfc.ac.uk/news-events/3d-volume-data-visualisation-feb14 3pm, Friday 31st January 2014 tn_tncJan-13.jpg "NIRFAST: An interactive GUI driven toolbox for modeling and image reconstruction in optical imaging" Hamid Dehghani. Nirfast is an FEM based package for modeling Near-Infrared light transport in tissue.This includes standard single wavelength absorption and scatter, multi-wavelength spectrally constrained models and fluorescence models. We will outline the development of NIRFAST for applications in diffuse optical imaging and provide examples of clinical and pre-clinical studies. The talk will highlight on unique features of NIRFAST, including pre-processing (volumetric meshing) to prediction of light propagation in biological media, as well as a set of novel image recovery algorithms. The meeting will start at 3pm in the Atlas Visualisation Facility. This can be found in the Atlas Building at Rutherford Appleton Laboratory on the Harwell Campus. https://eventbooking.stfc.ac.uk/news-events/3d-volume-data-visualisation-jan14

10am to 4pm, Friday 20th December 2013 tn_tncDec-13b.jpg Bring Your Own Data Day; "Do you have volume image data you'd like to analyse? Or do you have an analysis method that you want to make more efficient?" If so, come along to the CCPi Bring Your Data day at the Atlas Visualisation Facility at RAL on Dec 20th from 10am. We will provide help with image analysis using Avizo and Avizo Fire whether it's image registration, thresholding, segmentation or extracting data from the image. Atlas Building – Atlas Visualisation Facility https://eventbooking.stfc.ac.uk/news-events/3d-volume-data-visualisation-dec13 3pm, Friday 29th November 2013 tn_tncNov-13b.jpg CCPi Image Quantification Tools – within VolView and Avizo: presented by David Worth. Available from the CCPi CCPForge repository: VolView and Avizo" Download modules from: http://ccpforge.cse.rl.ac.uk/gf/project/iqa/frs/ Atlas Building – Atlas Visualisation Facility https://eventbooking.stfc.ac.uk/news-events/3d-volume-data-visualisation-nov13

3pm, Friday 25th October 2013 tn_tncOct-13.jpg 3D Volume Data Visualisation: Software show-and-tell. The open-source drishti visualiser: examples and ideas from desktop to power-wall. Atlas Building – Atlas Visualisation Facility https://eventbooking.stfc.ac.uk/news-events/3d-volume-data-visualisation 3pm, Friday 27th September 2013 tn_tncSep-13.jpg The Hartree Centre in collaboration with Harwell Imaging Partnership (HIP) has now opened a new facility for visualisation in the Atlas building at RAL. This is located in the CR08 room which is fully refurbished and fitted with an immersive 3D system including head tracking. We have a dedicated team of technical experts who are able to help users to port their applications and data to the 3D display and also in their data analysis needs. Seminars consisting of a short talks/show-and-tells along with opportunity to discuss visualisation needs with your data.

Friday 20th August 2013 tn_tncAug-13.jpg The Hartee Centre in collaboration with Harwell Imaging Partnership (HIP) has opened a visualisation facility in the Atlas building in RAL. This is located in the CR08 room which is fully refurbished and fitted with an immersive 3D system including head tracking.The aim is for software sharing and dissemination; and to this end a three year software contract for Avizo (3D Volume Visualisation from VSG[FEI]) has been purchased across SCD, DLS and RCaH.There is a dedicated 10GbE network connection between this room and the Hartree Centre’s IBM BlueGene and Blue Wonder computers at Daresbury Lab for visualising application results. This facility also has two high memory visualisation machine each with ½ TB RAM. They are installed with most of the popular open source visualisation applications and some commercial applications including Avizo (http://www.vsg3d.com/avizo/overview); ideal for example for quantitative visualisation of tomographic image volumes as collected at Diamond.

Meeting List 2015-2016: Tomo-Coffee and training vis events; so far, 9 attendees.

  • Novitom inc at RAL and link to Manchester 12 September 2016 [8+1](9)
  • Lucia Mancini 7 October 2016 (28)
  • Mark Basham, Imano Luengo, Michele Darrow SuRVoS? 31 January 2017 (29; 24+5)
  • Hamish Carr 9 February 2017 (16)
  • Flagship meeting 20 March 2017 ()
  • ...

Total first three years - 551 attendees

Meeting List 2015-2016: Tomo-Coffee and ParaView events; 184+ attendees.

  • Seminars alternative to an Away Day up to ToScA in Manchester for 2 September 2015 (27)
  • Monday 19 October 2015 - DREAM3D? (9+4+??)
  • Friday 30 October 2015 - Antoniu Pop (11)
  • Thursday 26 November 2015 - Not yet becoming IronMan – but software for Touchable Scientific Visualisations (12)
  • Monday 14 December 2015 - Bring and discsuss your own data and see the Virtual reality visualsation (RAL only) (5)
  • Wednesday 13 January 2016 - Jakob Sauer Jorgensen (10)
  • 16 March 2016 - Michael McCarthy? (NPL) (31)
  • 9 June 2016 - Fringe Meeting (15)
  • 6 July, 11 July and 14 July 2016 - special meetings for vis review (??)
  • Friday 11 August 2016 - CCPi Interactive Vis (12)
  • Friday 11 July 2016 - TIGRE launch (10)
  • 12 September 2016 (4 + 9) 8 September 2016 (14) TomViz.org demonstrator [29]

Meeting List 2014-2015: Tomo-Coffee and ParaView events; 203 attendees.

  • Paraview - 28 August 2014 TomViz (18) Meet the author
  • Monday 8 September 2014 Drishti visualiser - Meet the author (am 15; pm 5)
  • Friday 26 September 2014 "Image-based simulation of diffusion and flows within experimental volumetric data sets" Dr Marcus Campbell Bannerman, University of Aberdeen (26)
  • Friday 10 October 2014 Russell Garwood "Open source software for visualising tomographic datasets" (16)
  • Wednesday 26 November 2014. Sam Worthington (Worthington Sharpe Ltd.) Title "Wing: Beyond the mouse". At Daresbury Labs (STFC) A1 Rylands (10)
  • Friday 12 December 2014 - Talk by Prof Sarah Hainsworth, University of Leicester(27+)
  • Thursday 18 December 2014 - Data and Visualisation Needs Survey , Martin Turner, Tim Morris and Ron Fowler (9)
  • Friday 27 February 2015 - Fast X-ray reconstructioon and IMAT framework (18+3+5 - three site meetings)
  • Friday 27 March 2015 - Image Analysis program from NOCTYlab (10)
  • Friday 24 April 2015 - Avizo VR Module Demonstration (7) Extra session on 7 May 2015 (8)
  • Open Day events on 8-11 July 2015, pre-event (6)
  • Seminars alternative to an Away Day up to ToScA? in Manchester for 2 September 2015 (27)

Season 2013-2014: 12 Tomo-Coffee events and one ParaView event; 164 attendees. Meeting List:

  • Pre-meeting to check software suitability on 20 August 2013 (4)
  • Friday 27 September 2013 "Vis Software - Commercial to Open Source" (23)
  • Friday 25 October 2013 volume visualisation with drishti (14)
  • Friday 29 November 2013 "Quantitative Visualisation from the CCPi CCPForge repository: VolView and Avizo" Download modules from: http://ccpforge.cse.rl.ac.uk/gf/project/iqa/frs/ (17)
  • Friday 20 December 2013 Data show and understand session (8)
  • Friday 31 January 2014 NIRFAST (12)
  • Friday 28 February 2014 MANTID (11)
  • Paraview - 19 March 2104 Intro (6)
  • Friday 28 March 2014 LaVision (24)
  • Thursday 8 May 2014 Avizo 8.1 8.01 training course (14)
  • Friday 30 May 2013 Paraview as Volume Visualisation (14)
  • Thursday 26 June 2014 Diamond DAWN system (5) [Friday 25 April Diamond DAWN system (Postponed - 4)]
  • Friday 1 August 2014 Data show and understand session (12, inc demos)

Possible topics:

  • CCPi - Reconstruction techniques
  • Facilities available; eg RCaH
  • Conferences and Links eg ToScA
  • Other Segmentation methods and experience
  • Company presentations
  • etc ...

Atlas Visualisation Facility: available to staff of STFC, Diamond, RCaH and also their users. For further information and booking;

https://wiki.e-science.cclrc.ac.uk/web1/bin/view/VisualisationCentre/AtlasRoom

Srikanth Nagella (srikanth.nagella@stfc.ac.uk), Ron Fowler (ronald.fowler@stfc.ac.uk) or Martin Turner (martin.turner@stfc.ac.uk)


Paraview and Related Vis Tools Forum – Pre-session held over a lunch at Wednesday 5 March 1pm.

Paraview Forum (DL) 19 March 2014, 3pm 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 http://www.paraview.org/. 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.

Paraview Forum (DL) 16 April 2014, 3pm _Postponed_

ParaView Forum (DL) Meeting 28 August 2014, 2pm: A branded ParaView-based application, called tomviz by Marcus D. Hanwell et al.: "with a focus on 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: http://www.tomviz.org/ 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."

Session at Daresbury Labs on Wednesday 29 April 2015.


SCD Seminar Series: Visualisation, VR and Computer Graphics topics presented at DL-RAL. See main site and announcements for full details.

SCD Seminar 27 February 2015. 3pm-4pm - "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 http://stfc.ac.uk/SCD/research/data/44593.aspx

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. '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

Coffee-and-Tomo Session: 3pm-4pm: 10 October 2014 - Talk by Russell Garwood in R89 (S44) 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: martin.turner@stfc.ac.uk

3pm, 27 August 2014 SCD Seminar hosted by Tom Keal, CCP5/BioSIM: "Avogadro 2: Scaling to Large Systems, Improving Code Integration and Chemical Data Informatics/Analytics" Location: STFC sites: Arkwright A23 (2nd Floor) DL & VC Link to S44/R89 RAL

Abstract: Avogadro 2 is a complete rewrite of the Avogadro project, with a suite of targeted software libraries, and 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.

A tour of the libraries (many of which are entirely non-graphical and can be used on supercomputers etc), and new extension mechanisms will offer a broad overview of new features. These include dynamic Python extensions for input generation and file input/output, a data-centric interface and a switch to an interface that natively supports many molecules. Initial progress in areas such as client-server computing, scene graphs for chemistry, and integration of the Visualization Toolkit will be demonstrated.

MoleQueue will be described, an application for running external codes, submitting jobs to high performance computing resources and monitoring execution. MonogChem offers chemical data storage, indexing, search and informatics, with both companion applications using a simple local communication protocol for seamless integration. MongoChemWeb also enables wider sharing of chemical data, sharing many of the same resources. Finally an overview of the software process, and collaborative R&D model will be described.

11am, 1 August 2014 University of Hull Immersive Visualisation Environment (17)

Developments at the Hull Immersive Visualization Environment (HIVE) Helen Wright will describe some present and some future work going on at the University of Hull.

Abstract: 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.

Software by James Ward to enable quad buffer stereo in Unity, on Windows or Linux; that has been released in full source-code form on Google code: https://code.google.com/p/quadifier/

10am, 18 December 2013 HIP Meeting ()

SCD Interactions with the Harwell Imaging Partnership Mike Curtis-Rouse and Joe Kelleher at RAL will describe some present and some future interactions between the Harwell Imaging Partnership and SCD.

Abstract: 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.

3pm, 10 December 2013 CCP meeting ()

Whale to Turbine Impact Simulated Using CUDA Based Smoothed Particle Hydrodynamics on GPUs: 10 December 2013, 3pm Stephen Longshaw, University of Manchester

Abstract: 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). Tuesday 10 December 2013 at 3pm VC Link; 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.

2:15pm, 19 November 2013 CCP meeting ()

CCP 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 & BP ICAM

Abstract: 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.

2pm, 14 October 2013 Vis Meeting ()

Mashhuda Glencross, lecturer in the Vision Imaging and Autonomous Systems (VIAS) group at Loughborough University. Title: 'Relightable Buildings from Photographs and Beyond'

Abstract: In this talk I will describe previous work at Loughborough University on creating perceptually high quality 3D reconstructions of real outdoor scenes. I will also outline more recent work to build a material reflectance acquisition setup, and how this setup will be used to study material perception. I will conclude with the requirements for perceptually validated material models within the automotive industry, outlined in a recent industry position paper.

10am, 10th October 2013 Vis Meeting ()

Michael Adrian, 'Uses of 3DVIA Studio Pro Virtual Reality system'

Abstract: 3DVIA Studio Pro is an interactive 3D application authoring platform that empowers users to efficiently create and flexibly deliver visually stunning, immersive 3DEXPERIENCES. Michael Adrian will provide a brief overview of 3DVIA Studio Pro software with a focus on engineering and science applications. There will be an opportunity for a Q&A session.


Training Courses:

FEI at RAL 3 November 2015 and give a short tutorial on Avizo in the AVF (14)

Avizo course at Manchester, 3 November 2015 (18)

18 September 2015 Brian Bay and Loic Courtois organising a DVC workshop in the Atlas Visualisation Facility (12?)

2 September 2015 Avizo training course (22)

2 September 2015 Drishti/Prayog training course - New topics and advanced use within version 2.6 of Drishti (26)

MXIF Avizo course at Manchester 18-19 August (10)

Diamond Manchester Collaboration et al. Visualisation and quantification of tomographic data 28-29 July 2015 (20)

Introduction of Avizo course at Manchester; 9 June 2015 (24)

29 May 2015 "Imasim Pro" software overview (10)

12 May 2015, Avizo Visit at RAL held in AVF (Atlas Visualisation Facility) R27 (12)

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.

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). http://www.pet-mri.eu/PETMR_School_15.html

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.

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

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

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 nick.draper@stfc.ac.uk

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

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

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

22 October 2014 - 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 http://ccpforge.cse.rl.ac.uk/gf/project/cgls

Introduction to the Software Engineering Support Centre and CCPForge: Tuesday, 7th October 2014. Related to CCPs etc. https://eventbooking.stfc.ac.uk/news-events/introduction-to-the-software-engineering-support-centre-and-ccpforge-230

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.

8 September 2015 Drishti one-day special consultation event

21-25 July 2014 and 27 July - 1 August 2014 Hartee Summer Schools

22 July 2014 Developers' day at Nottingham (14). Including away-day tour of the new Hounsfield Facility

14-18 July 2014 Hartee Summer School in Visualisation

Avizo visualisation course at the Diamond House (15), 16-17 July 2014; via the RCaH/Diamond Consortium

11-13 June 2014 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

3-6 June 2014 MXIF introductory courses: Introduction to X-ray Computed Tomography (XCT) and AVIZO standard on the 3 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

20 May 2014 Developers' day at Birmingham

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)

28-29 January 2014 Avizo and CT course UoM

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

15-17 January 2014 Avizo and CT course DLS/STFC

14 January 2014 Developers' day at Birmingham

12 December DVC training course by RCaH at RAL

29 October - 1 November 2013, Avizo and CT course UoM

8-10 October 2013, 3DVIA Studio Pro held at DL

7-8 October 2013, Avizo (VSG) held at RAL

24-26 June 2013, Avizo (VSG) held at RAL

-- MartinTurner - 11 Sep 2013

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