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Extra Specialist Seminars:Monday 10 June 2019 - Joe Kelleher EnginX - part of the CCPi Working Group meeting: video conference event ‘Neutron diffraction and imaging on Engin-X for multi-scale characterisation’. Abstract: Characterisation and analysis of engineering structures from the atomic up to the macroscale is often needed for a full understanding of their behaviour. Neutrons are a versatile probe for such characterisation, as the wavelengths of neutrons needed for diffraction from common crystalline materials can easily achieve penetrations of several centimetres in common engineering materials. Here, we show examples of engineering research on the Engin-X instrument at the ISIS Pulsed Neutron Source, while also demonstrating how these may be combined with complementary measurements on other instruments.*8 March 2018* Manchester Inverse Imaging Goup Seminar: Alan Turing Building, Frank Adams 2 at 2pm Prof Bill Lionheart "Histotomography" | ||||||||
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Extra Specialist Seminars:Monday 10 June 2019 - Joe Kelleher EnginX - part of the CCPi Working Group meeting: video conference event ‘Neutron diffraction and imaging on Engin-X for multi-scale characterisation’. Abstract: Characterisation and analysis of engineering structures from the atomic up to the macroscale is often needed for a full understanding of their behaviour. Neutrons are a versatile probe for such characterisation, as the wavelengths of neutrons needed for diffraction from common crystalline materials can easily achieve penetrations of several centimetres in common engineering materials. Here, we show examples of engineering research on the Engin-X instrument at the ISIS Pulsed Neutron Source, while also demonstrating how these may be combined with complementary measurements on other instruments.*8 March 2018* Manchester Inverse Imaging Goup Seminar: Alan Turing Building, Frank Adams 2 at 2pm Prof Bill Lionheart "Histotomography" | ||||||||
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| < < | Abstracts: CIL software availability - October Meeting
There’s a top-level overview here http://www.ccpi.ac.uk/cil
Bit more guidance including installation instructions here https://github.com/vais-ral/CCPi-Framework
(growing) documentation is here http://edosil.net/stfc/cil/html/index.html
and a number of demos to get started are here https://github.com/vais-ral/CIL-Demos | |||||||
| > > | Abstracts: CIL software availability - December Meeting
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| this includes demos with Nikon data sets exemplified by the Sophiabeads data here https://github.com/vais-ral/CIL-Demos/tree/master/Tomography/Real%20Data/Cone%20Beam
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Revision 21201 Aug 2019 - MartinTurner
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Revision 21123 Jul 2019 - MartinTurner
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| < < | Tuesday 9 July 2019 - Mike White / Bill Lionheart and Mario Sandoval Olive | |||||||
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| > > | There’s a top-level overview here http://www.ccpi.ac.uk/cil | |||||||
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| < < | Mike White - Title: Helgason-Ludwig Consistency Conditions Abstract: The Helgason-Ludwig consistency conditions provide a means to test the validity of parallel-beam data, acquired from either an X-ray or neutron source. Simulations of various forms of error have been computed and research is now being done to determine whether a diagnosis of the error can be successfully implemented using the Helgason-Ludwig consistency conditions. | |||||||
| > > | Bit more guidance including installation instructions here https://github.com/vais-ral/CCPi-Framework | |||||||
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| < < | Mario Sandoval Olive - Title: Controlling 3D visualisations with multiple controllers Abstract: The talk will highlight the current state of the development of a new multi-layer framework ideal for two-handed interaction in desktop virtual environments, and we report some of our initial results. Another way to control Drishti | |||||||
| > > | (growing) documentation is here http://edosil.net/stfc/cil/html/index.html
and a number of demos to get started are here https://github.com/vais-ral/CIL-Demos
this includes demos with Nikon data sets exemplified by the Sophiabeads data here https://github.com/vais-ral/CIL-Demos/tree/master/Tomography/Real%20Data/Cone%20Beam | |||||||
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Lunch-and-Learn Sessions; often 12 noon - second Tuesday of the Month in Manchester (Royce Institute - Alan Turing Building / PSI)Schedule: | ||||||||
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| Mike White - Title: Helgason-Ludwig Consistency Conditions Abstract: The Helgason-Ludwig consistency conditions provide a means to test the validity of parallel-beam data, acquired from either an X-ray or neutron source. Simulations of various forms of error have been computed and research is now being done to determine whether a diagnosis of the error can be successfully implemented using the Helgason-Ludwig consistency conditions. | ||||||||
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| < < | Mario Sandoval Olive - Title LISU: Library for Interactive Settings of User-Modes Abstract: A new multi-layered framework for multimodal interactions. Another way to control Drishti | |||||||
| > > | Mario Sandoval Olive - Title: Controlling 3D visualisations with multiple controllers Abstract: The talk will highlight the current state of the development of a new multi-layer framework ideal for two-handed interaction in desktop virtual environments, and we report some of our initial results. Another way to control Drishti | |||||||
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| < < | Monday 10 June 2019 - Joe Kelleher EnginX - part of the CCPi Working Group meeting: video conference event ‘Neutron diffraction and imaging on Engin-X for multi-scale characterisation’. Abstract: Characterisation and analysis of engineering structures from the atomic up to the macroscale is often needed for a full understanding of their behaviour. Neutrons are a versatile probe for such characterisation, as the wavelengths of neutrons needed for diffraction from common crystalline materials can easily achieve penetrations of several centimetres in common engineering materials. Here, we show examples of engineering research on the Engin-X instrument at the ISIS Pulsed Neutron Source, while also demonstrating how these may be combined with complementary measurements on other instruments.*8 March 2018* Manchester Inverse Imaging Goup Seminar: Alan Turing Building, Frank Adams 2 at 2pm Prof Bill Lionheart "Histotomography" | |||||||
| > > | Monday 10 June 2019 - Joe Kelleher EnginX - part of the CCPi Working Group meeting: video conference event ‘Neutron diffraction and imaging on Engin-X for multi-scale characterisation’. Abstract: Characterisation and analysis of engineering structures from the atomic up to the macroscale is often needed for a full understanding of their behaviour. Neutrons are a versatile probe for such characterisation, as the wavelengths of neutrons needed for diffraction from common crystalline materials can easily achieve penetrations of several centimetres in common engineering materials. Here, we show examples of engineering research on the Engin-X instrument at the ISIS Pulsed Neutron Source, while also demonstrating how these may be combined with complementary measurements on other instruments.*8 March 2018* Manchester Inverse Imaging Goup Seminar: Alan Turing Building, Frank Adams 2 at 2pm Prof Bill Lionheart "Histotomography" | |||||||
| 12 March 2019 Lunch-and-Learn 12noon in Manchester, RAL and video-conf | ||||||||
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| < < | Tuesday 9 July 2019 - Mike White / Bill Lionheart presentation on the Helgason-Ludwig consistency conditions, and Drishti-interface project, Mario Sandoval Olive | |||||||
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| < < | Abstracts here soon. | |||||||
| > > | Abstracts: | |||||||
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| < < | Monday 10 June 2019 - Joe Kelleher EnginX - part of the CCPi Working Group meeting: video conference event ‘Neutron diffraction and imaging on Engin-X for multi-scale characterisation’. Abstract: Characterisation and analysis of engineering structures from the atomic up to the macroscale is often needed for a full understanding of their behaviour. Neutrons are a versatile probe for such characterisation, as the wavelengths of neutrons needed for diffraction from common crystalline materials can easily achieve penetrations of several centimetres in common engineering materials. Here, we show examples of engineering research on the Engin-X instrument at the ISIS Pulsed Neutron Source, while also demonstrating how these may be combined with complementary measurements on other instruments. | |||||||
| > > | Mike White - Title: Helgason-Ludwig Consistency Conditions Abstract: The Helgason-Ludwig consistency conditions provide a means to test the validity of parallel-beam data, acquired from either an X-ray or neutron source. Simulations of various forms of error have been computed and research is now being done to determine whether a diagnosis of the error can be successfully implemented using the Helgason-Ludwig consistency conditions. Mario Sandoval Olive - Title LISU: Library for Interactive Settings of User-Modes Abstract: A new multi-layered framework for multimodal interactions. Another way to control Drishti | |||||||
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| < < | 8 March 2018 Manchester Inverse Imaging Goup Seminar: Alan Turing Building, Frank Adams 2 at 2pm Prof Bill Lionheart "Histotomography" | |||||||
| > > | Monday 10 June 2019 - Joe Kelleher EnginX - part of the CCPi Working Group meeting: video conference event ‘Neutron diffraction and imaging on Engin-X for multi-scale characterisation’. Abstract: Characterisation and analysis of engineering structures from the atomic up to the macroscale is often needed for a full understanding of their behaviour. Neutrons are a versatile probe for such characterisation, as the wavelengths of neutrons needed for diffraction from common crystalline materials can easily achieve penetrations of several centimetres in common engineering materials. Here, we show examples of engineering research on the Engin-X instrument at the ISIS Pulsed Neutron Source, while also demonstrating how these may be combined with complementary measurements on other instruments.*8 March 2018* Manchester Inverse Imaging Goup Seminar: Alan Turing Building, Frank Adams 2 at 2pm Prof Bill Lionheart "Histotomography" | |||||||
| 12 March 2019 Lunch-and-Learn 12noon in Manchester, RAL and video-conf | ||||||||
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Revision 20525 Jun 2019 - MartinTurner
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| > > | Recent and next Seminars: Tuesday 9 July 2019 - Mike White / Bill Lionheart presentation on the Helgason-Ludwig consistency conditions, and Drishti-interface project, Mario Sandoval Olive Abstracts here soon. | |||||||
| Monday 10 June 2019 - Joe Kelleher EnginX - part of the CCPi Working Group meeting: video conference event ‘Neutron diffraction and imaging on Engin-X for multi-scale characterisation’. Abstract: Characterisation and analysis of engineering structures from the atomic up to the macroscale is often needed for a full understanding of their behaviour. Neutrons are a versatile probe for such characterisation, as the wavelengths of neutrons needed for diffraction from common crystalline materials can easily achieve penetrations of several centimetres in common engineering materials. Here, we show examples of engineering research on the Engin-X instrument at the ISIS Pulsed Neutron Source, while also demonstrating how these may be combined with complementary measurements on other instruments. | ||||||||
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Lunch-and-Learn Sessions; often 12 noon - second Tuesday of the Month in Manchester (Royce Institute - Alan Turing Building / PSI)Schedule: | ||||||||
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| < < | Monday 10 June 2019 - Joe Kelleher EnginX - part of the CCPi Working Group meeting: video conference event ‘Neutron diffraction and imaging on Engin-X for multi-scale characterisation’. Abstract: Characterisation and analysis of engineering structures from the atomic up to the macroscale is often needed for a full understanding of their behaviour. Neutrons are a versatile probe for such characterisation, as the wavelengths of neutrons needed for diffraction from common crystalline materials can easily achieve penetrations of several centimetres in common engineering materials. Here, we show examples of engineering research on the Engin-X instrument at the ISIS Pulsed Neutron Source, while also demonstrating how these may be combined with complementary measurements on other instruments. | |||||||
| > > | Monday 10 June 2019 - Joe Kelleher EnginX - part of the CCPi Working Group meeting: video conference event ‘Neutron diffraction and imaging on Engin-X for multi-scale characterisation’. Abstract: Characterisation and analysis of engineering structures from the atomic up to the macroscale is often needed for a full understanding of their behaviour. Neutrons are a versatile probe for such characterisation, as the wavelengths of neutrons needed for diffraction from common crystalline materials can easily achieve penetrations of several centimetres in common engineering materials. Here, we show examples of engineering research on the Engin-X instrument at the ISIS Pulsed Neutron Source, while also demonstrating how these may be combined with complementary measurements on other instruments. | |||||||
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| < < | Monday 10 June 2019 - Joe Kelleher EnginX - part of the CCPi Working Group meeting: video conference event. | |||||||
| > > | Monday 10 June 2019 - Joe Kelleher EnginX - part of the CCPi Working Group meeting: video conference event ‘Neutron diffraction and imaging on Engin-X for multi-scale characterisation’. Abstract: Characterisation and analysis of engineering structures from the atomic up to the macroscale is often needed for a full understanding of their behaviour. Neutrons are a versatile probe for such characterisation, as the wavelengths of neutrons needed for diffraction from common crystalline materials can easily achieve penetrations of several centimetres in common engineering materials. Here, we show examples of engineering research on the Engin-X instrument at the ISIS Pulsed Neutron Source, while also demonstrating how these may be combined with complementary measurements on other instruments. | |||||||
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| < < | Monday 3 June 2019 - Jason Wong “Challenges of imaging for trauma reconstruction- how you can help” Abstract- The talk will highlight the current state of the clinical art in terms of imaging that guides clinical decision making in trauma, and identifies where there are great unmet needs and opportunities to influence how clinical decision making is made in the trauma reconstruction setting. And Kathy Christofidou. | |||||||
| > > | Monday 10 June 2019 - Joe Kelleher EnginX - part of the CCPi Working Group meeting: video conference event. | |||||||
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Past and present seminar information including links for visualisation.Seminars and vis sessions (http://tinyurl.com/STFCVisSem) across the sites: | ||||||||
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| < < | 3 June 2019 Jason Wong and Kathy Christofidou. | |||||||
| > > | Monday 3 June 2019 - Jason Wong “Challenges of imaging for trauma reconstruction- how you can help” Abstract- The talk will highlight the current state of the clinical art in terms of imaging that guides clinical decision making in trauma, and identifies where there are great unmet needs and opportunities to influence how clinical decision making is made in the trauma reconstruction setting. And Kathy Christofidou. | |||||||
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| Total first three years - 551 attendees Meeting List 2015-2016: Tomo-Coffee and ParaView events; 184+ attendees. | ||||||||
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| 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. | ||||||||
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| < < | 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 | |||||||
| > > | 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). <a target="_top" href="http://www.pet-mri.eu/PETMR_School_15.html" style="color: #666666; font-family: arial, verdana, sans-serif; font-size: 13.6499996185303px; line-height: 20.4749984741211px; background-color: #ffffff">http://www.pet-mri.eu/PETMR_School_15.html</a> | |||||||
| 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. | ||||||||
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| < < | 14 May 2019: Wen Zhang Title: Investigation of fatigue overload retardation mechanisms in Ni as a function of grain size Abstract: Overload fatigue test results are presented for high purity nickel with grain sizes ranging from micrometres down to nanometres. Synchrotron X-ray diffraction (SXRD) and digital image correlation (DIC) were applied in situ to map the through-thickness strain field and surface displacement field respectively before, during and after overload. The variation in residual stress and stress intensity factor (SIF) was evaluated from the diffraction strain field while the changes of crack length, crack opening displacement and SIF range were determined from the DIC displacement field. Retardation was observed for all the samples at low stress ratio (R=0.1). The fatigue crack growth (FCG) for the microcrystalline sample (grain size greater than 1 µm) was the most retarded after overload because of its more tortuous and rougher crack surface, larger overload plastic zone and hence more significant crack face contact. While for the nanocrystalline sample (grain size below 100 nm) the FCG was least affected by overload due to the relatively straight and flat crack surface, very small plastic zone size and therefore limited residual stress and no evident crack closure. The decrease in FCG for ultrafine grained (UFG) nickel (with grain size between 1 µm and 100 nm) is not only resulted from overload-induced residual stress and crack closure, but also the crack deflection caused by the anisotropic microstructure. More significant residual stress and crack closure were observed for the UFG sample with elongated microstructure aligned perpendicular to the crack propagation direction. and Katrine Bangsgaard Title TBA | |||||||
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| Abstract: Overload fatigue test results are presented for high purity nickel with grain sizes ranging from micrometres down to nanometres. Synchrotron X-ray diffraction (SXRD) and digital image correlation (DIC) were applied in situ to map the through-thickness strain field and surface displacement field respectively before, during and after overload. The variation in residual stress and stress intensity factor (SIF) was evaluated from the diffraction strain field while the changes of crack length, crack opening displacement and SIF range were determined from the DIC displacement field. Retardation was observed for all the samples at low stress ratio (R=0.1). The fatigue crack growth (FCG) for the microcrystalline sample (grain size greater than 1 µm) was the most retarded after overload because of its more tortuous and rougher crack surface, larger overload plastic zone and hence more significant crack face contact. While for the nanocrystalline sample (grain size below 100 nm) the FCG was least affected by overload due to the relatively straight and flat crack surface, very small plastic zone size and therefore limited residual stress and no evident crack closure. The decrease in FCG for ultrafine grained (UFG) nickel (with grain size between 1 µm and 100 nm) is not only resulted from overload-induced residual stress and crack closure, but also the crack deflection caused by the anisotropic microstructure. More significant residual stress and crack closure were observed for the UFG sample with elongated microstructure aligned perpendicular to the crack propagation direction. | ||||||||
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| < < | Abstract: Overload fatigue test results are presented for high purity nickel with grain sizes ranging from micrometres down to nanometres. Synchrotron X-ray diffraction (SXRD) and digital image correlation (DIC) were applied in situ to map the through-thickness strain field and surface displacement field respectively before, during and after overload. The variation in residual stress and stress intensity factor (SIF) was evaluated from the diffraction strain field while the changes of crack length, crack opening displacement and SIF range were determined from the DIC displacement field. Retardation was observed for all the samples at low stress ratio (R=0.1). The fatigue crack growth (FCG) for the microcrystalline sample (grain size greater than 1 µm) was the most retarded after overload because of its more tortuous and rougher crack surface, larger overload plastic zone and hence more significant crack face contact. While for the nanocrystalline sample (grain size below 100 nm) the FCG was least affected by overload due to the relatively straight and flat crack surface, very small plastic zone size and therefore limited residual stress and no evident crack closure. The decrease in FCG for ultrafine grained (UFG) nickel (with grain size between 1 µm and 100 nm) is not only resulted from overload-induced residual stress and crack closure, but also the crack deflection caused by the anisotropic microstructure. More significant residual stress and crack closure were observed for the UFG sample with elongated microstructure aligned perpendicular to the crack propagation direction. | |||||||
| > > | Abstract: Overload fatigue test results are presented for high purity nickel with grain sizes ranging from micrometres down to nanometres. Synchrotron X-ray diffraction (SXRD) and digital image correlation (DIC) were applied in situ to map the through-thickness strain field and surface displacement field respectively before, during and after overload. The variation in residual stress and stress intensity factor (SIF) was evaluated from the diffraction strain field while the changes of crack length, crack opening displacement and SIF range were determined from the DIC displacement field. Retardation was observed for all the samples at low stress ratio (R=0.1). The fatigue crack growth (FCG) for the microcrystalline sample (grain size greater than 1 µm) was the most retarded after overload because of its more tortuous and rougher crack surface, larger overload plastic zone and hence more significant crack face contact. While for the nanocrystalline sample (grain size below 100 nm) the FCG was least affected by overload due to the relatively straight and flat crack surface, very small plastic zone size and therefore limited residual stress and no evident crack closure. The decrease in FCG for ultrafine grained (UFG) nickel (with grain size between 1 µm and 100 nm) is not only resulted from overload-induced residual stress and crack closure, but also the crack deflection caused by the anisotropic microstructure. More significant residual stress and crack closure were observed for the UFG sample with elongated microstructure aligned perpendicular to the crack propagation direction. and Katrine Bangsgaard Title TBA | |||||||
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| > > | 14 May 2019: Wen Zhang Title: Investigation of fatigue overload retardation mechanisms in Ni as a function of grain size
Abstract: Overload fatigue test results are presented for high purity nickel with grain sizes ranging from micrometres down to nanometres. Synchrotron X-ray diffraction (SXRD) and digital image correlation (DIC) were applied in situ to map the through-thickness strain field and surface displacement field respectively before, during and after overload. The variation in residual stress and stress intensity factor (SIF) was evaluated from the diffraction strain field while the changes of crack length, crack opening displacement and SIF range were determined from the DIC displacement field. Retardation was observed for all the samples at low stress ratio (R=0.1). The fatigue crack growth (FCG) for the microcrystalline sample (grain size greater than 1 µm) was the most retarded after overload because of its more tortuous and rougher crack surface, larger overload plastic zone and hence more significant crack face contact. While for the nanocrystalline sample (grain size below 100 nm) the FCG was least affected by overload due to the relatively straight and flat crack surface, very small plastic zone size and therefore limited residual stress and no evident crack closure. The decrease in FCG for ultrafine grained (UFG) nickel (with grain size between 1 µm and 100 nm) is not only resulted from overload-induced residual stress and crack closure, but also the crack deflection caused by the anisotropic microstructure. More significant residual stress and crack closure were observed for the UFG sample with elongated microstructure aligned perpendicular to the crack propagation direction. | |||||||
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| < < | 12 March 2019 Lunch-and-Learn 12noon in Manchester, RAL and video-conf
Please register here: https://forms.office.com/Pages/ResponsePage.aspx?id=HDZmP36oWEGPYZnoLbPKyIoNg6mJSW5Jp6v4v7D_cv9UNFZIOEtCOVdLU0k4T0pCQjBVWTE0MVpCRy4u
Dan Symes and Ceri Brenner:
"Tomographic imaging using intense laser-driven radiation sources": High power lasers (> 100 TW) can be used as the driver for compact light sources that deliver extreme brightness ultrashort x-ray pulses ideally suited for advanced imaging applications. The laser is used to create a cm-scale plasma accelerator generating femtosecond relativistic electron bunches with GeV? energy that can be converted to x-ray beams through a plasma betatron process or bremsstrahlung radiation. This produces up to 1010 photons per pulse in the x-ray region spanning 10 keV up to multi-MeV. The beam is spatially coherent because of the micron-scale source size, enabling phase enhanced imaging to improve contrast between low Z materials with similar density. Using the Gemini laser at RAL we have demonstrated high resolution micro-CT of biological samples and NDE of industrial components. The same laser can generate x-ray energies in the 10’s keV range for soft tissue, low density polymer and composite materials and in the multi-MeV range for penetration of large dense samples such as automotive or aerospace components. Commercialisation of high power laser technology has led to robust, well-characterised systems that are relatively compact and affordable. In the next few years, we expect to develop laser-plasma accelerators as dedicated x-ray machines, capable of micron resolution tomography with high frame rate. This shift from conducting proof-of-principle experiments to operating a synchrotron-style beam brings challenges for our research community – it is necessary for us to build expertise in handling large datasets, image processing, and tomographic reconstruction. We will present the status of CT using laser-driven sources with a view to discussion of how we can engage with the imaging community and what new opportunities may arise for the CCPi network.dimensional-XCT conference update from Huddersfield, Paul Bills A Hartree Perspective: Working with STFC Opportunities - Tim Kirkham (12:45pm) The Bridging for Innovators https://www.stfc.ac.uk/b4iIntroduction new staff and description of ICT'2019, Gemma Fardell ...presenting her experiences to data including work at Nikon Metrolgy and plans for the future - also review of iCT ...'very application heavy this year. Every other year it is based in Wels, and ... little more research orientated. The industry talks only take up one morning, and there was a lot of input from research groups around Europe. This year ~350 attendees, so the conference is probably the largest XCT one in Europe - there were a couple of posters on multi-spectral CT, and reconstruction is always a popular topic." | |||||||
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| 8 March 2018 Manchester Inverse Imaging Goup Seminar: Alan Turing Building, Frank Adams 2 at 2pm Prof Bill Lionheart "Histotomography" | ||||||||
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| > > | 12 March 2019 Lunch-and-Learn 12noon in Manchester, RAL and video-conf
Please register here: https://forms.office.com/Pages/ResponsePage.aspx?id=HDZmP36oWEGPYZnoLbPKyIoNg6mJSW5Jp6v4v7D_cv9UNFZIOEtCOVdLU0k4T0pCQjBVWTE0MVpCRy4u
Dan Symes and Ceri Brenner:
"Tomographic imaging using intense laser-driven radiation sources": High power lasers (> 100 TW) can be used as the driver for compact light sources that deliver extreme brightness ultrashort x-ray pulses ideally suited for advanced imaging applications. The laser is used to create a cm-scale plasma accelerator generating femtosecond relativistic electron bunches with GeV? energy that can be converted to x-ray beams through a plasma betatron process or bremsstrahlung radiation. This produces up to 1010 photons per pulse in the x-ray region spanning 10 keV up to multi-MeV. The beam is spatially coherent because of the micron-scale source size, enabling phase enhanced imaging to improve contrast between low Z materials with similar density. Using the Gemini laser at RAL we have demonstrated high resolution micro-CT of biological samples and NDE of industrial components. The same laser can generate x-ray energies in the 10’s keV range for soft tissue, low density polymer and composite materials and in the multi-MeV range for penetration of large dense samples such as automotive or aerospace components. Commercialisation of high power laser technology has led to robust, well-characterised systems that are relatively compact and affordable. In the next few years, we expect to develop laser-plasma accelerators as dedicated x-ray machines, capable of micron resolution tomography with high frame rate. This shift from conducting proof-of-principle experiments to operating a synchrotron-style beam brings challenges for our research community – it is necessary for us to build expertise in handling large datasets, image processing, and tomographic reconstruction. We will present the status of CT using laser-driven sources with a view to discussion of how we can engage with the imaging community and what new opportunities may arise for the CCPi network.dimensional-XCT conference update from Huddersfield, Paul Bills A Hartree Perspective: Working with STFC Opportunities - Tim Kirkham (12:45pm) The Bridging for Innovators https://www.stfc.ac.uk/b4iIntroduction new staff and description of ICT'2019, Gemma Fardell ...presenting her experiences to data including work at Nikon Metrolgy and plans for the future - also review of iCT ...'very application heavy this year. Every other year it is based in Wels, and ... little more research orientated. The industry talks only take up one morning, and there was a lot of input from research groups around Europe. This year ~350 attendees, so the conference is probably the largest XCT one in Europe - there were a couple of posters on multi-spectral CT, and reconstruction is always a popular topic." | |||||||
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| < < | Seminars and vis sessions (http://tinyurl.com/STFCVisSem) across the sites. | |||||||
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| > > | Please register here: https://forms.office.com/Pages/ResponsePage.aspx?id=HDZmP36oWEGPYZnoLbPKyIoNg6mJSW5Jp6v4v7D_cv9UNFZIOEtCOVdLU0k4T0pCQjBVWTE0MVpCRy4u | |||||||
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| < < | "Tomographic imaging using intense laser-driven radiation sources": High power lasers (> 100 TW) can be used as the driver for compact light sources that deliver extreme brightness ultrashort x-ray pulses ideally suited for advanced imaging applications. The laser is used to create a cm-scale plasma accelerator generating femtosecond relativistic electron bunches with GeV? energy that can be converted to x-ray beams through a plasma betatron process or bremsstrahlung radiation. This produces up to 1010 photons per pulse in the x-ray region spanning 10 keV up to multi-MeV. The beam is spatially coherent because of the micron-scale source size, enabling phase enhanced imaging to improve contrast between low Z materials with similar density. Using the Gemini laser at RAL we have demonstrated high resolution micro-CT of biological samples and NDE of industrial components. The same laser can generate x-ray energies in the 10’s keV range for soft tissue, low density polymer and composite materials and in the multi-MeV range for penetration of large dense samples such as automotive or aerospace components. Commercialisation of high power laser technology has led to robust, well-characterised systems that are relatively compact and affordable. In the next few years, we expect to develop laser-plasma accelerators as dedicated x-ray machines, capable of micron resolution tomography with high frame rate. This shift from conducting proof-of-principle experiments to operating a synchrotron-style beam brings challenges for our research community – it is necessary for us to build expertise in handling large datasets, image processing, and tomographic reconstruction. We will present the status of CT using laser-driven sources with a view to discussion of how we can engage with the imaging community and what new opportunities may arise for the CCPi network. | |||||||
| > > | "Tomographic imaging using intense laser-driven radiation sources": High power lasers (> 100 TW) can be used as the driver for compact light sources that deliver extreme brightness ultrashort x-ray pulses ideally suited for advanced imaging applications. The laser is used to create a cm-scale plasma accelerator generating femtosecond relativistic electron bunches with GeV? energy that can be converted to x-ray beams through a plasma betatron process or bremsstrahlung radiation. This produces up to 1010 photons per pulse in the x-ray region spanning 10 keV up to multi-MeV. The beam is spatially coherent because of the micron-scale source size, enabling phase enhanced imaging to improve contrast between low Z materials with similar density. Using the Gemini laser at RAL we have demonstrated high resolution micro-CT of biological samples and NDE of industrial components. The same laser can generate x-ray energies in the 10’s keV range for soft tissue, low density polymer and composite materials and in the multi-MeV range for penetration of large dense samples such as automotive or aerospace components. Commercialisation of high power laser technology has led to robust, well-characterised systems that are relatively compact and affordable. In the next few years, we expect to develop laser-plasma accelerators as dedicated x-ray machines, capable of micron resolution tomography with high frame rate. This shift from conducting proof-of-principle experiments to operating a synchrotron-style beam brings challenges for our research community – it is necessary for us to build expertise in handling large datasets, image processing, and tomographic reconstruction. We will present the status of CT using laser-driven sources with a view to discussion of how we can engage with the imaging community and what new opportunities may arise for the CCPi network. | |||||||
| dimensional-XCT conference update from Huddersfield, Paul Bills A Hartree Perspective: Working with STFC Opportunities - Tim Kirkham (12:45pm) | ||||||||
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The Bridging for Innovators https://www.stfc.ac.uk/b4i programme runs across all STFC facilities and gives business the opportunity to work with STFC facilities and Scientists on up to a full funded basis. There is an opportunity to strengthen links between STFC and Universities by businesses linked to Universities working on this programme to combine expertise. Such an opportunity exists potentially at centres such as the Royce, and this talk will give an over view of this opportunity and welcome ideas to stimulate collaboration.
Introduction new staff and description of ICT'2019, Gemma Fardell | ||||||||
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| Video Streamed to PSI Seminar Room (3.306, Alan Turing building) at University of Manchester - local host martin.turner@manchester.ac.uk | ||||||||
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| 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. | ||||||||
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| < < | 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 …). | |||||||
| > > | 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. | ||||||||
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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. | ||||||||
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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. | ||||||||
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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. | ||||||||
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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. | ||||||||
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| < < | 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. | |||||||
| > > | 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. | |||||||
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| < < | 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 | |||||||
| > > | 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 | |||||||
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| < < | 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)” | |||||||
| > > | 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)” | |||||||
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2:00pm-3:00pm: Wednesday 13 January 2016 - Jakob Sauer Jřrgensen, 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. | ||||||||
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| < < | 3:00pm-4:30pm: Monday 14 December 2015 - "“Bring/Discuss-Your-Own-Data" and see Virtual Reality visualisation" RAL Atlas Visualisation Facility | |||||||
| > > | 3:00pm-4:30pm: Monday 14 December 2015 - "“Bring/Discuss-Your-Own-Data" and see Virtual Reality visualisation" RAL Atlas Visualisation Facility | |||||||
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| < < | 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 | |||||||
| > > | 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 | |||||||
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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) | ||||||||
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2pm-3pm: Friday 19 October 2015 - Video Conferencing Mike Groeber Presentation on the general overview of DREAM.3D" http://dream3d.bluequartz.net/?p=1313 | ||||||||
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| Season 2013-2014: 12 Tomo-Coffee events and one ParaView event; 164 attendees. Meeting List: | ||||||||
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| Srikanth Nagella (srikanth.nagella@stfc.ac.uk), Ron Fowler (ronald.fowler@stfc.ac.uk) or Martin Turner (martin.turner@stfc.ac.uk)
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| < < | Paraview and Related Vis Tools Forum – Pre-session held over a lunch at Wednesday 5 March 1pm. | |||||||
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| < < | 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) 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_ | ||||||||
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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. | ||||||||
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| < < | ... 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 | |||||||
| > > | ... 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 | ||||||||
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| < < | 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 | |||||||
| > > | 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 | ||||||||
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| 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. | ||||||||
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| < < | 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. | |||||||
| > > | 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 () | ||||||||
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| Cryo-Ops 2014 held was big success with 93 people viewing- although in three sessions. November 12, 2014 | ||||||||
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| < < | 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 | |||||||
| > > | 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 | |||||||
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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 | ||||||||
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| < < | 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. | |||||||
| > > | 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 | ||||||||
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| Avizo visualisation course at the Diamond House (15), 16-17 July 2014; via the RCaH/Diamond Consortium | ||||||||
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| < < | 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 | |||||||
| > > | 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 | |||||||
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| < < | 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 | |||||||
| > > | 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 | ||||||||
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| < < | 12 March 2019 Lunch-and-Learn 12noon in Manchester adn video-conf to RAL | |||||||
| > > | 12 March 2019 Lunch-and-Learn 12noon in Manchester, RAL and video-conf Please register here: https://forms.office.com/Pages/ResponsePage.aspx?id=HDZmP36oWEGPYZnoLbPKyIoNg6mJSW5Jp6v4v7D_cv9UNFZIOEtCOVdLU0k4T0pCQjBVWTE0MVpCRy4u | |||||||
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| "Tomographic imaging using intense laser-driven radiation sources": High power lasers (> 100 TW) can be used as the driver for compact light sources that deliver extreme brightness ultrashort x-ray pulses ideally suited for advanced imaging applications. The laser is used to create a cm-scale plasma accelerator generating femtosecond relativistic electron bunches with GeV? energy that can be converted to x-ray beams through a plasma betatron process or bremsstrahlung radiation. This produces up to 1010 photons per pulse in the x-ray region spanning 10 keV up to multi-MeV. The beam is spatially coherent because of the micron-scale source size, enabling phase enhanced imaging to improve contrast between low Z materials with similar density. Using the Gemini laser at RAL we have demonstrated high resolution micro-CT of biological samples and NDE of industrial components. The same laser can generate x-ray energies in the 10’s keV range for soft tissue, low density polymer and composite materials and in the multi-MeV range for penetration of large dense samples such as automotive or aerospace components. Commercialisation of high power laser technology has led to robust, well-characterised systems that are relatively compact and affordable. In the next few years, we expect to develop laser-plasma accelerators as dedicated x-ray machines, capable of micron resolution tomography with high frame rate. This shift from conducting proof-of-principle experiments to operating a synchrotron-style beam brings challenges for our research community – it is necessary for us to build expertise in handling large datasets, image processing, and tomographic reconstruction. We will present the status of CT using laser-driven sources with a view to discussion of how we can engage with the imaging community and what new opportunities may arise for the CCPi network. | ||||||||
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| < < | dimensional-XCT conference update from Huddersfield, Paul Bills Abstract to come: | |||||||
| > > | dimensional-XCT conference update from Huddersfield, Paul Bills
A Hartree Perspective: Working with STFC Opportunities - Tim Kirkham (12:45pm)
The Bridging for Innovators https://www.stfc.ac.uk/b4i | |||||||
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12 March 2019 Lunch-and-Learn 12noon in Manchester adn video-conf to RAL
Dan Symes and Ceri Brenner:
"Tomographic imaging using intense laser-driven radiation sources": High power lasers (> 100 TW) can be used as the driver for compact light sources that deliver extreme brightness ultrashort x-ray pulses ideally suited for advanced imaging applications. The laser is used to create a cm-scale plasma accelerator generating femtosecond relativistic electron bunches with GeV? energy that can be converted to x-ray beams through a plasma betatron process or bremsstrahlung radiation. This produces up to 1010 photons per pulse in the x-ray region spanning 10 keV up to multi-MeV. The beam is spatially coherent because of the micron-scale source size, enabling phase enhanced imaging to improve contrast between low Z materials with similar density. Using the Gemini laser at RAL we have demonstrated high resolution micro-CT of biological samples and NDE of industrial components. The same laser can generate x-ray energies in the 10’s keV range for soft tissue, low density polymer and composite materials and in the multi-MeV range for penetration of large dense samples such as automotive or aerospace components. Commercialisation of high power laser technology has led to robust, well-characterised systems that are relatively compact and affordable. In the next few years, we expect to develop laser-plasma accelerators as dedicated x-ray machines, capable of micron resolution tomography with high frame rate. This shift from conducting proof-of-principle experiments to operating a synchrotron-style beam brings challenges for our research community – it is necessary for us to build expertise in handling large datasets, image processing, and tomographic reconstruction. We will present the status of CT using laser-driven sources with a view to discussion of how we can engage with the imaging community and what new opportunities may arise for the CCPi network.dimensional-XCT conference update from Huddersfield, Paul Bills Abstract to come: Introduction new staff and description of ICT'2019, Gemma Fardell ...presenting her experiences to data including work at Nikon Metrolgy and plans for the future - also review of iCT ...'very application heavy this year. Every other year it is based in Wels, and ... little more research orientated. The industry talks only take up one morning, and there was a lot of input from research groups around Europe. This year ~350 attendees, so the conference is probably the largest XCT one in Europe - there were a couple of posters on multi-spectral CT, and reconstruction is always a popular topic." | |||||||
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Extra Specialist Seminars:8 March 2018 Manchester Inverse Imaging Goup Seminar: Alan Turing Building, Frank Adams 2 at 2pm Prof Bill Lionheart "Histotomography" | ||||||||
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| 30 January 2018 (Tuesday) 2pm at AVF in RAL and 1 February 2018 (Thursday) 2pm at Frank Adams 2, Alan Turing Building, University of Manchester. Visiting Flagship speaker: Dr. Joan Duran
18 January 2018 Software show-and-tell for TomViz? (from kitware Inc.) tomography processing and visualisation: moving from electron tomography to XCT and neutron tomography http://www.ccpi.ac.uk/node/363http://www.ccpi.ac.uk/node/363 | ||||||||
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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 | ||||||||
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| < < | 8 March 2018 Manchester Inverse Imaging Goup Seminar: Alan Turing Building, Frank Adams 2 at 2pm Prof Bill Lionheart "Histotomography" | |||||||
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| < < | 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 the University of Manchester MXIF at 12noon with pizza | |||||||
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| > > | SCD (STFC) based Seminars:6 July 2018 9:30am pre-coffee talk - Remote Visualisation and Analysis of Tomographic Data - Providing Near Data Analysis Environments and Visualisation for Diamond Data; Richard Smith at RAL and DL campuses 4 July 2018 Seminar on Digital Volume Correlation by Prof. Brian Bay (Oregon State University). Abstract: Digital Volume Correlation (DVC) | |||||||
| 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. | ||||||||
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8 February 2018 SCD Seminar "Geometric Measures of Isocontour Regions" Hamish Carr University of Leeds https://www.ccpi.ac.uk/node/381https://www.ccpi.ac.uk/node/381
30 January 2018 (Tuesday) 2pm at AVF in RAL and 1 February 2018 (Thursday) 2pm at Frank Adams 2, Alan Turing Building, University of Manchester. Visiting Flagship speaker: Dr. Joan Duran
18 January 2018 Software show-and-tell for TomViz? (from kitware Inc.) tomography processing and visualisation: moving from electron tomography to XCT and neutron tomography http://www.ccpi.ac.uk/node/363http://www.ccpi.ac.uk/node/363 | |||||||
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
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| < < | 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 | |||||||
| > > | 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. | ||||||||
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| 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.
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| < < | 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 | |||||||
| > > | 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 | ||||||||
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| < < | 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. | |||||||
| > > | 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 | ||||||||
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| 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. | ||||||||
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| < < | Lunch and Learn sessions at Manchester MXIF | |||||||
| > > | Lunch and Learn sessions at Manchester MXIF at 12non with pizza | |||||||
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| < < | CCPi Flagship Meeting 2pm-4pm - open sessions from 3pm at RAL 20 March 2017 | |||||||
| > > | 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 | |||||||
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| < < | 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. | |||||||
| > > | 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. | |||||||
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| < < | FEI at RAL 3 November and give a short tutorial on Avizo in the AVF (14) | |||||||
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| < < | Avizo course at Manchester, 3 November (18) | |||||||
| > > | 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?) | ||||||||
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| < < | Seminars and vis sessions (http://tinyurl.com/STFCVisSem) across the two sites. | |||||||
| > > | 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. | ||||||||
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| > > | Lunch and Learn sessions at Manchester MXIF | |||||||
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Meeting List 2015-2016: Tomo-Coffee and training vis events; so far, 9 attendees.
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Total first three years - 551 attendees
Meeting List 2015-2016: Tomo-Coffee and ParaView events; 184+ attendees.
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| 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. | ||||||||
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| < < | Provisional - 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' Time to be announced. Held at RAL and via Video Conference. | |||||||
| > > | 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. | |||||||
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| < < | 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. | |||||||
| > > | 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 | ||||||||
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Meeting List 2015-2016: Tomo-Coffee and training vis events; so far, 9 attendees.
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Meeting List 2015-2016: Tomo-Coffee and training vis events; so far, 9 attendees.
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Revision 14513 Jan 2017 - MartinTurner
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| > > | Provisional - 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' Time to be announced. 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. | ||||||||
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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. | ||||||||
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| < < | 31 January 2016 Software Show-and-Tell 2pm in the RAL Atlas Visualisation Facility: Mark Baham et al., SuRVoS (Super-Region Volume Segmentation) Workbench is a new software for semi-automated segmentation of 3D image volumes. It has been developed jointly between the University of Nottingham, UK and Diamond Light Source, UK and is open source: https://diamondlightsource.github.io/SuRVoS/ | |||||||
| > > | 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.
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| < < | 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." | |||||||
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31 January 2016 Software Show-and-Tell 2pm in the RAL Atlas Visualisation Facility: Mark Baham et al., SuRVoS (Super-Region Volume Segmentation) Workbench is a new software for semi-automated segmentation of 3D image volumes. It has been developed jointly between the University of Nottingham, UK and Diamond Light Source, UK and is open source: https://diamondlightsource.github.io/SuRVoS/
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."
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. | ||||||||
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| < < | 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 will be made available as a podcast: contact for details (martin.turner@manchester.ac.uk) | |||||||
| > > | 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. | ||||||||
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| < < | Visiting CCPi Fellow; Friday 7 October 2016 Seminar 1pm in University of Manchester, Williamson Building, School of Earth and Environmental Sciences, room G03. "Advanced 3D and 4D X-ray imaging techniques for the morphological and textural analysis of geomaterials" Lucia Mancini1 Elettra-Sincrotrone Trieste S.C.p.A., 34149 Basovizza (Trieste), Italy beamline scientists of the SYRMEP beamline at the Elettra synchrotron light source. This will be made available as a podcast: contact for details (martin.turner@manchester.ac.uk) | |||||||
| > > | 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 will be made available as a podcast: contact for details (martin.turner@manchester.ac.uk) | |||||||
| 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. | ||||||||
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Meeting List 2014-2015: Tomo-Coffee and ParaView events; 203 attendees.
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| > > | Visiting CCPi Fellow; Friday 7 October 2016 Seminar 1pm in University of Manchester, Williamson Building, School of Earth and Environmental Sciences, room G03. "Advanced 3D and 4D X-ray imaging techniques for the morphological and textural analysis of geomaterials" Lucia Mancini1 Elettra-Sincrotrone Trieste S.C.p.A., 34149 Basovizza (Trieste), Italy beamline scientists of the SYRMEP beamline at the Elettra synchrotron light source. This will be made available as a podcast: contact for details (martin.turner@manchester.ac.uk) 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. | |||||||
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| < < | Meeting List 2015-2016: Tomo-Coffee and ParaView events; so far, 40+ attendees.
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| < < | 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 | |||||||
| > > | Twelve Tomography Seminars for the Season 2015-2016 all in one picture:
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| < < | 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. | |||||||
| > > | 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. | |||||||
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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. | ||||||||
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| > > | 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 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. | |||||||
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.
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| < < | 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 to Whitworth Room in DL - local host Sri Nagella. | |||||||
| > > | 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. | |||||||
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| < < | 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 to Whitworth Room in DL - local host Sri Nagella. | |||||||
| > > | 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. | |||||||
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| > > | 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 to Whitworth Room in DL - local host Sri Nagella. | |||||||
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| < < | 2:00pm-3:30pm: Friday 11 August 2016 CCPi Interactive Vis - Show-and-Tell https://github.com/CERN/TIGRE RAL AVF (Atlas Visualisation Facility), Whitworth Room in DL and Bluejeans Video Conference link - local host Sri Nagella.
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2:00pm-3:30pm: Friday 11 August 2016 CCPi Interactive Vis - Show-and-Tell https://github.com/CERN/TIGRE RAL AVF (Atlas Visualisation Facility), Whitworth Room in DL and Bluejeans Video Conference link - local host Sri Nagella.
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| 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
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| > > | 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 | |||||||
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| < < | 6 July 2016, 2:00pm-3:00pm 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. | |||||||
| > > | 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. | |||||||
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| < < | 6 July 2016, 2:00pm-3:00pm 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. | |||||||
| > > | 6 July 2016, 2:00pm-3:00pm 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. | |||||||
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| < < | 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 | |||||||
| > > | 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 | |||||||
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| < < | 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)” | |||||||
| > > | 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)” | |||||||
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| > > | 6 July 2016, 2:00pm-3:00pm 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 Jřrgensen, 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.
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| < < | PROVISIONAL SEMINAR: 2:00pm-3:00pm Wednesday 13 January 2016 Jakob Sauer Jřrgensen Limited-data X-ray tomography and sparsity regularization Abstract: In this seminar I will give an overview of some recent results and ongoing projects within limited-data X-ray tomographic reconstruction and sparsity regularization. First, I will describe a special limited angle tomography problem in which metal bar sample holders cause cone-shaped parts missing in the sinogram. I will describe our attempts of characterizing and preliminary results of removing the resulting artifacts. Next, I will present a projection matching algorithm for automatically aligning tomographic projections of unknown exact orientation. In the present case we are interested in ultra-high resolution tomographic reconstruction from ptychography data. Currently, unknown sample translations and rotations at the nano-scale for example caused by vibration limit the achievable reconstruction quality. I will show preliminary results with simulated and real synchrotron ptychography data. Finally, I will mention our attempts of establishing a connection between image sparsity and the amount of undersampling admitted by sparsity-regularized reconstrution 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 point to a potential follow-up study for validation on real data using the SophiaBeads data set recently released from the University of Manchester | |||||||
| > > | 2:00pm-3:00pm: Wednesday 13 January 2016 - Jakob Sauer Jřrgensen, 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.
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| < < | 2:00pm-3:00pm Wednesday 13 January 2016 Jakob Sauer Jřrgensen Limited-data X-ray tomography and sparsity regularization Abstract: In this seminar I will give an overview of some recent results and ongoing projects within limited-data X-ray tomographic reconstruction and sparsity regularization. First, I will describe a special limited angle tomography problem in which metal bar sample holders cause cone-shaped parts missing in the sinogram. I will describe our attempts of characterizing and preliminary results of removing the resulting artifacts. Next, I will present a projection matching algorithm for automatically aligning tomographic projections of unknown exact orientation. In the present case we are interested in ultra-high resolution tomographic reconstruction from ptychography data. Currently, unknown sample translations and rotations at the nano-scale for example caused by vibration limit the achievable reconstruction quality. I will show preliminary results with simulated and real synchrotron ptychography data. Finally, I will mention our attempts of establishing a connection between image sparsity and the amount of undersampling admitted by sparsity-regularized reconstrution 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 point to a potential follow-up study for validation on real data using the SophiaBeads data set recently released from the University of Manchester | |||||||
| > > | PROVISIONAL SEMINAR: 2:00pm-3:00pm Wednesday 13 January 2016 Jakob Sauer Jřrgensen Limited-data X-ray tomography and sparsity regularization Abstract: In this seminar I will give an overview of some recent results and ongoing projects within limited-data X-ray tomographic reconstruction and sparsity regularization. First, I will describe a special limited angle tomography problem in which metal bar sample holders cause cone-shaped parts missing in the sinogram. I will describe our attempts of characterizing and preliminary results of removing the resulting artifacts. Next, I will present a projection matching algorithm for automatically aligning tomographic projections of unknown exact orientation. In the present case we are interested in ultra-high resolution tomographic reconstruction from ptychography data. Currently, unknown sample translations and rotations at the nano-scale for example caused by vibration limit the achievable reconstruction quality. I will show preliminary results with simulated and real synchrotron ptychography data. Finally, I will mention our attempts of establishing a connection between image sparsity and the amount of undersampling admitted by sparsity-regularized reconstrution 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 point to a potential follow-up study for validation on real data using the SophiaBeads data set recently released from the University of Manchester | |||||||
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| < < | 3:00pm-4:30pm: Monday 14 December 2015 - "“Bring/Discuss-Your-Own-Data" and see Virtual Reality visualisation" RAL Atlas Visualisation Facility | |||||||
| > > | 2:00pm-3:00pm Wednesday 13 January 2016 Jakob Sauer Jřrgensen Limited-data X-ray tomography and sparsity regularization Abstract: In this seminar I will give an overview of some recent results and ongoing projects within limited-data X-ray tomographic reconstruction and sparsity regularization. First, I will describe a special limited angle tomography problem in which metal bar sample holders cause cone-shaped parts missing in the sinogram. I will describe our attempts of characterizing and preliminary results of removing the resulting artifacts. Next, I will present a projection matching algorithm for automatically aligning tomographic projections of unknown exact orientation. In the present case we are interested in ultra-high resolution tomographic reconstruction from ptychography data. Currently, unknown sample translations and rotations at the nano-scale for example caused by vibration limit the achievable reconstruction quality. I will show preliminary results with simulated and real synchrotron ptychography data. Finally, I will mention our attempts of establishing a connection between image sparsity and the amount of undersampling admitted by sparsity-regularized reconstrution 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 point to a potential follow-up study for validation on real data using the SophiaBeads data set recently released from the University of Manchester | |||||||
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| < < | 10:30pm-12noon: Friday 26 November 2015 - "Not yet becoming IronMan – but software for Touchable Scientific Visualisations" Martin Turner, Interactive Visualisation Group RAL Atlas Visualisation Facility | |||||||
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| > > | FEI at RAL 3 November and give a short tutorial on Avizo in the AVF (14) Avizo course at Manchester, 3 November (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 | ||||||||
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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)
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| < < | Seminars moving on an Away Day up to ToScA in Manchester for 2 September 2015 | |||||||
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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 on 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 | |||||||
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| < < | Open Day events on 8-11 July 2015 - Showing 3D visualisation for various topics to over a thousand visitors.
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| < < | 2pm-3pm: Friday 24 April 2015 - Avizo Virtual Reality Module for Collaborative and Immersive VR – Now Touch Your Tomographic Volume
RAL Atlas Visualisation Facility – Live demo so you need to be there, and please bring your own data!
Local host for this event is Sri Nagella (srikanth.nagella@stfc.ac.uk)
2pm-3pm: Friday 27 March 2015 - Image processing software, NOCTYlab, show-and-tell from NOCTYLIO (http://www.noctylio.com/ ) "Noctylio is a software start-up company located in Bordeaux; its purpose is to open up new horizons in 3D imaging."
Local host for this event is Sri Nagella (srikanth.nagella@stfc.ac.uk)
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| < < | 3:00pm-3:30pm: Friday 27 February 2015 - "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 and to ICAM in University of Manchester.
3:30pm-4:00pm: Friday 27 February 2015 - "Update and SCD view of the ICP: IMAT Computing Project " Sri Nagella and Erica Yang, @Room S44 in R89 at RAL and Video conference to Arkwright room in DL and to ICAM in University of Manchester.
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| < < | 2pm-3pm: Thursday 18 December 2014 - Data and Visualisation Needs Survey , Martin Turner, Tim Morris and Ron Fowler @RAL in R89/Access Grid and room A1 in DL
First half for Tomography Seminars for the Season 2013-2014 all in one picture:
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| < < | Meeting List 2014-2015: Tomo-Coffee and ParaView events; so far, 40+ attendees. | |||||||
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Season 2013-2014: 12 Tomo-Coffee events and one ParaView event; 164 attendees. Meeting List:
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| < < | 19 October VC seminar: Mike Groeber "Presentation on the general overview of DREAM.3D" http://dream3d.bluequartz.net/?p=1313 | |||||||
| > > | 2pm-3pm: Friday 19 October 2015 - Video Conferencing Mike Groeber Presentation on the general overview of DREAM.3D" http://dream3d.bluequartz.net/?p=1313
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| < < | Abstract: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. | |||||||
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| < < | 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. | |||||||
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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) Abstract: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. 19 October VC seminar: Mike Groeber "Presentation on the general overview of DREAM.3D" http://dream3d.bluequartz.net/?p=1313 | |||||||
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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) | ||||||||
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| < < | 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 | |||||||
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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) | ||||||||
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| < < | 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 1:30pm-4:30pm Avizo training course: 2 workflows related to analysis of fibrous materials will be presented. The second use-case is based on 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) | |||||||
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| > > | Seminars moving on an Away Day up to ToScA in Manchester for 2 September 2015
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 - Showing 3D visualisation for various topics to over a thousand visitors. | |||||||
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| SCD Seminar Series: Visualisation, VR and Computer Graphics topics presented at DL-RAL. See main site and announcements for full details. | ||||||||
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| < < | 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. | |||||||
| > > | 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. | |||||||
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... 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 | ||||||||
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| > > | 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. | ||||||||
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RAL Atlas Visualisation Facility – Live demo so you need to be there, and please bring your own data!
Local host: Sri Nagella (srikanth.nagella@stfc.ac.uk)
"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.
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2pm-3pm: Friday 27 March 2015 - Image processing software, NOCTYlab, show-and-tell from NOCTYLIO (http://www.noctylio.com/) "Noctylio is a software start-up company located in Bordeaux; its purpose is to open up new horizons in 3D imaging." | ||||||||
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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." | ||||||||
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SCD Seminar Series: Visualisation, VR and Computer Graphics topics presented at DL-RAL. See main site and announcements for full details. | ||||||||
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| > > | 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. | ||||||||
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| Srikanth Nagella (srikanth.nagella@stfc.ac.uk), Ron Fowler (ronald.fowler@stfc.ac.uk) or Martin Turner (martin.turner@stfc.ac.uk)
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2pm-3pm: Friday 27 March 2015 - Image processing software, NOCTYlab, show-and-tell from NOCTYLIO (http://www.noctylio.com/ ) "Noctylio is a software start-up company located in Bordeaux; its purpose is to open up new horizons in 3D imaging." | ||||||||
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