Tomographic Imaging
Lead Research Organisation:
The University of Manchester
Department Name: Materials
Abstract
Computed Tomography (CT) is a powerful non-destructive evaluation (NDE) technique for producing 2-D cross-sections and 3-D images of an object from a series of 2D projections (shadowgraphs).
Critical to the process is the computer algorithms that are able to pre-process and then reconstruct the 3D images from many (often over thousands) shadowgraphs. There are three critical steps to obtaining useful information from tomography i) the correction and calibration stage starting from initial image capture, ii) the reconstruction of a 3D image from these 2D projections and iii) the analysis and quantification of features in the 3D object.
While the techniques are rapidly growing in popularity, most users have fairly limited options when trying to recover the 3D image and are able to write only fairly primitive computer programs to extract key features from the images. The aim of this CCP is to establish a framework within which different reconstruction algorithms, artefact reduction codes, and image analysis procedures are made available to all.
Critical to the process is the computer algorithms that are able to pre-process and then reconstruct the 3D images from many (often over thousands) shadowgraphs. There are three critical steps to obtaining useful information from tomography i) the correction and calibration stage starting from initial image capture, ii) the reconstruction of a 3D image from these 2D projections and iii) the analysis and quantification of features in the 3D object.
While the techniques are rapidly growing in popularity, most users have fairly limited options when trying to recover the 3D image and are able to write only fairly primitive computer programs to extract key features from the images. The aim of this CCP is to establish a framework within which different reconstruction algorithms, artefact reduction codes, and image analysis procedures are made available to all.
Planned Impact
Economy
At present there are 1,000s of x-ray radiography machines operating in industry, primarily at Airports but also for quality inspection. Fast CT machines coupled with automatic threat or defect recognition will replace radiography over the next few years. It is anticipated that components from the three toolkits developed will lead to at least three industrial studies to develop applications specific to industrial companies. Industrial attendees will be encouraged to assist and participate in the training and science workshops and administration will be expected to identify from our industrial partners the key issues from their perspective prior to developing the toolkit algorithms. The CCP covers a much broader range of tomography applications and industrial users; consequently the uptake is expected to be far greater than this (see Critical Success Factors). As the CCP continues to develop it will broadens its remit into other tomographic applications (already contacts with PET and Neutron Tomography) so this industrial focussed community will grow.
Knowledge
This Tomographic Imaging CCP will benefit; ESRF and Diamond Light Source x-ray imaging users, ISIS Neutron and Muon spallation users and those with access to laboratory x-ray facilities
EPSRC Software as an Infrastructure strategy
Not only does this CCP assist and aid some of the major national facilities but also utilises related infrastructures including compute clusters within STFC and in the regions. Following the quote "Better Software Better Research" we have members who have fellowships within the SSI (Software sustainability Institute); and working within the CCP_FORGE.
In the first phase we have taken opportunities to increase skills by collaborating and sharing expertise including, new multi-grid methods exploited with developers in the CCP_ASEArch and a case study with the Harwell Imaging Partnership. We are also aware of the further overlaps with proposed CCPs including; CCP_PET/MR, CCP_VISUK, and CCP_EM. Internationally we have representation and collaboration with the Europe (EU COST action) and have links with the US Argon National Labs (APS software stack).
Society
The project will deliver benefit in the many areas including Medical Imaging. Image guided radiation therapy (IGRT) equipment with integrated kilo-voltage X-ray cone-beam CT underpins the standard of care recommended by the National Radiotherapy Advisory Group in 2007. Improved image quality will be essential to support dynamic tumour targeting, treatment intervention and adaptation. One pathway to impact in this area will be the production of 3 highlights videos each year to be made available to the Network community to communicate the benefits of the project to stakeholders, to inspire young people in STEM subjects and to raise awareness of the general public.
People
The groups at Manchester and Bath have a strong record of developing young researchers. For example, 12 of Prof. Withers students have gone on to lectureships/Chairs elsewhere and 6 more are now instrument scientists, while at Imperial 6 of Prof. Lee's are now lecturers or Chairs (e.g. at CMU, Tsinghua, NTU), as well as key industrialists, worldwide. Involvement in a multidisciplinary community is expected to provide an incubator for new scientists and engineers on the Harwell site.
Finally, visual information can be a great aid to understanding ('seeing is believing') so this project will deliver results that can be appreciated by the novice as well as the expert. To this end it will have a significant public engagement mission.
At present there are 1,000s of x-ray radiography machines operating in industry, primarily at Airports but also for quality inspection. Fast CT machines coupled with automatic threat or defect recognition will replace radiography over the next few years. It is anticipated that components from the three toolkits developed will lead to at least three industrial studies to develop applications specific to industrial companies. Industrial attendees will be encouraged to assist and participate in the training and science workshops and administration will be expected to identify from our industrial partners the key issues from their perspective prior to developing the toolkit algorithms. The CCP covers a much broader range of tomography applications and industrial users; consequently the uptake is expected to be far greater than this (see Critical Success Factors). As the CCP continues to develop it will broadens its remit into other tomographic applications (already contacts with PET and Neutron Tomography) so this industrial focussed community will grow.
Knowledge
This Tomographic Imaging CCP will benefit; ESRF and Diamond Light Source x-ray imaging users, ISIS Neutron and Muon spallation users and those with access to laboratory x-ray facilities
EPSRC Software as an Infrastructure strategy
Not only does this CCP assist and aid some of the major national facilities but also utilises related infrastructures including compute clusters within STFC and in the regions. Following the quote "Better Software Better Research" we have members who have fellowships within the SSI (Software sustainability Institute); and working within the CCP_FORGE.
In the first phase we have taken opportunities to increase skills by collaborating and sharing expertise including, new multi-grid methods exploited with developers in the CCP_ASEArch and a case study with the Harwell Imaging Partnership. We are also aware of the further overlaps with proposed CCPs including; CCP_PET/MR, CCP_VISUK, and CCP_EM. Internationally we have representation and collaboration with the Europe (EU COST action) and have links with the US Argon National Labs (APS software stack).
Society
The project will deliver benefit in the many areas including Medical Imaging. Image guided radiation therapy (IGRT) equipment with integrated kilo-voltage X-ray cone-beam CT underpins the standard of care recommended by the National Radiotherapy Advisory Group in 2007. Improved image quality will be essential to support dynamic tumour targeting, treatment intervention and adaptation. One pathway to impact in this area will be the production of 3 highlights videos each year to be made available to the Network community to communicate the benefits of the project to stakeholders, to inspire young people in STEM subjects and to raise awareness of the general public.
People
The groups at Manchester and Bath have a strong record of developing young researchers. For example, 12 of Prof. Withers students have gone on to lectureships/Chairs elsewhere and 6 more are now instrument scientists, while at Imperial 6 of Prof. Lee's are now lecturers or Chairs (e.g. at CMU, Tsinghua, NTU), as well as key industrialists, worldwide. Involvement in a multidisciplinary community is expected to provide an incubator for new scientists and engineers on the Harwell site.
Finally, visual information can be a great aid to understanding ('seeing is believing') so this project will deliver results that can be appreciated by the novice as well as the expert. To this end it will have a significant public engagement mission.
Publications
Abdullahi H
(2021)
Single droplets to particles - size, shape, shell thickness and porosity analyses using X-ray computed tomography
in Chemical Engineering Science
Alberto M
(2021)
High-grip and hard-wearing graphene reinforced polyurethane coatings
in Composites Part B: Engineering
Ametova E
(2021)
Crystalline phase discriminating neutron tomography using advanced reconstruction methods
in Journal of Physics D: Applied Physics
Andersen Martin S.
(2021)
Computed Tomography: Algorithms, Insight, and Just Enough Theory
Arzilli F
(2019)
Magma fragmentation in highly explosive basaltic eruptions induced by rapid crystallization
in Nature Geoscience
Baychev T
(2019)
Reliability of Algorithms Interpreting Topological and Geometric Properties of Porous Media for Pore Network Modelling
in Transport in Porous Media
Bhartiya A
(2020)
Phase-contrast 3D tomography of HeLa cells grown in PLLA polymer electrospun scaffolds using synchrotron X-rays.
in Journal of synchrotron radiation
| Description | The Collaborative project helped coordinate the 2018 X-ray CT Road-mapping exercise which along with town meetings and academic and industrial questionnaires led to the first assessment of the needs of the UK CT community. This has led to the development of a £10M National Research Facility which provides state of the art facilities for X-ray imaging for UK users and which works with the CCPi to train users in both introductory and advanced CT analysis and visualisation techniques. This project has maintained and reached out to a network of over 400 X-ray CT users from academia and industry. It has developed a toolbox of algorithms for the reconstruction and analysis of X-ray CT data (the Core imaging library). This open-source software for tomographic imaging has particular emphasis on reconstruction of challenging datasets, and is available to all UK users. The community are supported in deployment at large scale facilities (Diamond Light Source and ISIS neutron source) and lab X-ray CT systems. It has led to the development of new software particularly aimed at multi-channel (colour or hyper-spectral) CT. This software is now available at the IMAT neutron imaging facility at ISIS and will become available within the National Research Facility for colour X-ray CT. |
| Exploitation Route | Both the National Research Facility (NRF) which started in November 2020 and the renewal of this grant will provide the infrastructure to support a wide and vibrant UK X-ray CT community. Working with the National Large Scale Facilities, a wide range of in-situ experiments and multi-modal imaging experiments will be undertaken. Indeed up to 900 beam days will be made available for imaging per year through the NRF. The aims of the next phase of the CCPi grant are: 1. Better community: to strengthen links and collaboration across the UK X-CT community through networking activities, exchange visits and training; 2. Better tomography: to offer a step-change in the amount and quality of information provided by X-CT, by replacing proprietary black-box software with a unified open-source software framework, underpinning new applications in materials science, manufacturing, earth sciences and more; and 3. Better software, better research: in the words of the Software Sustainability Institute (SSI), to improve the reliability of research results through the use and championing of good software development practices including version control, testing, reproducibility, and documentation. It co-sponsors: 1) A technical tomo-week based at DLS, involving an Advances in X-ray Imaging Workshop and an associated Fringe Meeting (we regularly hold a co-located CIL hackathon). 2) Metrology tomo-events focussed on the NPL supported "dimensional-X-CT conference (DXCT)", where CCPi support training and also fund committee members from the BSI/ISO X-CT standards to attend. 3) The annual UK Tomography for Scientific Advancement (ToScA) symposium; a very popular user group meeting kick-started by the NHM and now being hosted by different educational or industrial institutes. Furthermore, the outputs of this grant are an essential part of the dissemination plan of our new ESPRC-funded International Centre-to-Centre project, 'Manufacturing by Design (MbD)'. Through the MbD we are developing an engineering component scanner set up at the ESRF which is able to image at unparalleled sample volume/voxel size ratios. The CCPi will provide the software tools to extract information from the data collected. |
| Sectors | Aerospace Defence and Marine Digital/Communication/Information Technologies (including Software) Energy Manufacturing including Industrial Biotechology Culture Heritage Museums and Collections Transport |
| URL | https://www.ccpi.ac.uk/ |
| Description | This grant has helped to support the emerging UK computed tomography community with a toolbox of algorithms to increase the quality and level of information. Over the course of the project the community has increased to over 400 members. The CCPi supports industry and the wider development of X-ray CT for digital metrology through the D-XCT conference and workshops. In 2019, our courses and workshops reached over 300 people. In 2020 and 2021 these moved online and we also ran a virtual seminar series which had 45 speakers and 369 attendees. Our training courses continue to serve the community and are now linked to the National Centre for X-Ray CT NXCT). This work has also led to a number of public engagement activities, including new software that explains the capabilities of X-ray CT. This software has been used to engage with the public at a number of Science Festivals including Bluedot (2018-20) and the Royal Society Summer Science Exhibition in 2020. |
| First Year Of Impact | 2015 |
| Sector | Aerospace, Defence and Marine,Energy,Healthcare,Manufacturing, including Industrial Biotechology,Culture, Heritage, Museums and Collections,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Cultural |
| Description | EPSRC Full College Membership |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Description | EPSRC XCT Equipment Roadmap Panel |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Description | Reader for BSI/ISO standard XCT TDF/4/4/1 |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Description | Alan Turing Institute: Event Support (Fringe Meeting - An Intelligent Framework: Pros and Cons of Al/ML in the Computed Tomography Pipeline) |
| Amount | £1,865 (GBP) |
| Organisation | Alan Turing Institute |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 05/2019 |
| End | 06/2019 |
| Description | EPSRC: Multiscale and In Situ Laboratory X-ray Computed Tomography National Research Facility |
| Amount | £10,000,000 (GBP) |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2020 |
| End | 07/2025 |
| Description | EPSRC: Tomographic Imaging: UK Collaborative Computational Projects |
| Amount | £296,693 (GBP) |
| Funding ID | EP/T026677/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2020 |
| End | 03/2025 |
| Description | National Research Facility for Lab X-ray CT |
| Amount | £10,097,652 (GBP) |
| Funding ID | EP/T02593X/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2020 |
| End | 10/2025 |
| Description | Research Software Engineer USA-UK Travel Fund (Software Sustainability Institute) |
| Amount | £2,500 (GBP) |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2017 |
| End | 09/2017 |
| Description | Rich Nonlinear Tomography for advanced materials (LEAD) |
| Amount | £635,422 (GBP) |
| Funding ID | EP/V007742/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2021 |
| End | 05/2024 |
| Title | Dynamic X-ray CT of Synthetic magma for Digital Volume Correlation analysis |
| Description | Dataset of synthetic magma subjected to compression, useful for Digital Volume Correlation analysis, ref [1,2]. The data has been acquired at the Diamond Light Source synchrotron, with a bespoke thermo-mechanical rig ("P2R") on the I12 beamline, ref [3,4,5]. Dataset 0 has no applied compression, while dataset 1 has applied compression. The data was saved with numpy 1.21 with NumPy format version 1.0 as dataset_0.npy and dataset_1.npy, and NumPy can be used to read it back in. Both data files have a header specifying how the data is stored, and following the header comes the array data. In particular the header length is 128 bytes, and the data consists of a 3 dimensional matrix of size (1520, 1257, 1260) stored in unsigned integer 8 bit, Fortran order. The screenshot named import_imagej.png shows how to import the data in with ImageJ. A METAImage header describing the data in text form for each dataset is also provided, i.e. dataset_0.mhd and dataset_1.mhd, |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/4835667 |
| Title | Hyperspectral X-ray CT Voxelized TV reconstruction of a single, iodine-stained lizard head sample |
| Description | Dataset description These datasets are voxel based reconstructions of hyperspectral CT data using the Core Imaging Library (CIL). They are stored as NeXus files (derived from hdf5) which can be read in, visualised and manipulated using CIL. - PDHG_TV_1000_Sp_alpha_0.004.nxs Is the solution after 1000 iterations of PDHG with TV applied in the spatial domain. - PDHG_TV_1000_SpCh_alpha_0.003_beta_0.5.nxs Is the solution after 1000 iterations of PDHG with TV applied both in the spatial domain, and in the energy (channel) domain. Dataset intended use These datasets are used in the CIL training notebook: https://github.com/TomographicImaging/CIL-Demos/blob/main/examples/3_Multichannel/03_Hyperspectral_reconstruction.ipynb They can be imported using CIL, with the following code snippet:
|
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | n/a |
| URL | https://zenodo.org/record/7016574 |
| Title | Hyperspectral X-ray CT Voxelized TV reconstruction of a single, iodine-stained lizard head sample |
| Description | Dataset description These datasets are voxel based reconstructions of hyperspectral CT data using the Core Imaging Library (CIL). They are stored as NeXus files (derived from hdf5) which can be read in, visualised and manipulated using CIL. - PDHG_TV_1000_Sp_alpha_0.004.nxs Is the solution after 1000 iterations of PDHG with TV applied in the spatial domain. - PDHG_TV_1000_SpCh_alpha_0.003_beta_0.5.nxs Is the solution after 1000 iterations of PDHG with TV applied both in the spatial domain, and in the energy (channel) domain. Dataset intended use These datasets are used in the CIL training notebook: https://github.com/TomographicImaging/CIL-Demos/blob/main/examples/3_Multichannel/03_Hyperspectral_reconstruction.ipynb They can be imported using CIL, with the following code snippet:
|
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/7016573 |
| Title | Hyperspectral X-ray CT data set of mineralised ore sample with Au and Pb deposits |
| Description | General data description: This is a hyperspectral (energy-resolved) X-ray CT projection data set of a mineralised ore sample with small gold and galena deposits. It was acquired in a laboratory micro-CT scanner with an energy-sensitive HEXITEC detector in the Henry Moseley X-ray Imaging Facility at The University of Manchester. The data included contains all the relevant files required for reconstruction, following a hyperspectral scan of a mineralised ore sample. The sample contains a number of mineral phases, of varying concentration, distributed throughout. Some phases (including gold, and lead-based Galena) produce unique absorption edges, which act as spectral identifiers that can be measured by an energy-sensitive detector. File descriptions: The data set consists of one .txt file and three .mat (MATLAB) data files. Au_rock_scan_geometry.txt gives a breakdown of the full sample and detector geometry used when acquiring the raw projections. The number of horizontal detector pixels accounts for the fact that a set of 5 tiled scans of the sample were collected and later stitched together. Au_rock_sinogram_full.mat contains the full 4D sinogram constructed following flat-field normalisation of the raw projection data. The data matrix contains the total number of energy channels acquired during scanning, as well as the conventional elements of vertical/horizontal detector pixel number and total projection angles. commonX.mat provides a direct conversion between the energy channels, and the energies (in keV) that they correspond to, following a calibration procedure prior to scanning. FF.mat contains the 4D flatfield data acquired when no sample was present. This data was used to normalise the projection datasets, as the sinogram was constructed. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/4157614 |
| Title | Hyperspectral X-ray CT data set of mineralised ore sample with Au and Pb deposits |
| Description | General data description: This is a hyperspectral (energy-resolved) X-ray CT projection data set of a mineralised ore sample with small gold and galena deposits. It was acquired in a laboratory micro-CT scanner with an energy-sensitive HEXITEC detector in the Henry Moseley X-ray Imaging Facility at The University of Manchester. The data included contains all the relevant files required for reconstruction, following a hyperspectral scan of a mineralised ore sample. The sample contains a number of mineral phases, of varying concentration, distributed throughout. Some phases (including gold, and lead-based Galena) produce unique absorption edges, which act as spectral identifiers that can be measured by an energy-sensitive detector. File descriptions: The data set consists of one .txt file and three .mat (MATLAB) data files. Au_rock_scan_geometry.txt gives a breakdown of the full sample and detector geometry used when acquiring the raw projections. The number of horizontal detector pixels accounts for the fact that a set of 5 tiled scans of the sample were collected and later stitched together. Au_rock_sinogram_full.mat contains the full 4D sinogram constructed following flat-field normalisation of the raw projection data. The data matrix contains the total number of energy channels acquired during scanning, as well as the conventional elements of vertical/horizontal detector pixel number and total projection angles. commonX.mat provides a direct conversion between the energy channels, and the energies (in keV) that they correspond to, following a calibration procedure prior to scanning. FF.mat contains the 4D flatfield data acquired when no sample was present. This data was used to normalise the projection datasets, as the sinogram was constructed. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | None |
| URL | https://zenodo.org/record/4157615 |
| Title | Hyperspectral X-ray CT dataset of a single, iodine-stained lizard head sample |
| Description | General Data description: This is a hyperspectral (energy-resolved) X-ray CT projection dataset of a lizard head sample, stained with an iodine contrast agent. It was acquired in a custom-built, laboratory micro-CT scanner with an energy-sensitive HEXITEC detector in the Henry Moseley X-ray Imaging Facility at The University of Manchester. The following data contains all the files necessary for reconstruction, after a hyperspectral scan was taken of a single, iodine-stained lizard head sample. The iodine contrast agent provided a spectral marker, measured by an energy-sensitive detector, which may be used for spatial mapping and segmentation of stained soft tissue regions. File descriptions: Contained are four MATLAB (.mat) data files, as well as a single text (.txt) file. Lizard_head_scan_parameters.txt provides the full sample and detector geometry of the scan acquisition. lizard_180Proj_noSupp_1_180.mat contains the full 4D sinogram constructed following flatfield normalisation of the raw projection data. The 4D array contains the total number of energy channels acquired during scanning, vertical and horizontal pixel number, and total projections angles acquired. The data provided is prior to application of any post-processing filters. The first 180 energy channels are included. lizard_180Proj_Supp_1_180.mat contains the full 4D sinogram constructed following flatfield normalisation of the raw projection data. This dataset is identical to the .mat file above, however here we have also applied a ring-reduction filter, using a wavelet-based Fourier filter which suppresses the presence of ring artefacts in every energy channel. The first 180 energy channels are included. Energy_axis.mat provides a direct conversion between the energy channels, and the energies (in keV) that they correspond to, following a calibration procedure prior to scanning. FF.mat contains the 4D flatfield data acquired when no sample was present. This data was used to normalise the projection datasets, as the sinogram was constructed. The first 180 energy channels are included. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | Not yet realised |
| URL | https://zenodo.org/record/4352943 |
| Title | Hyperspectral X-ray CT datasets for a set of multiply-stained mouse limb specimens |
| Description | General Data description: The following are hyperspectral (energy-resolved) X-ray CT datasets for a set of mouse limb specimens, each stained with multiple contrast agents. All scans were acquired with an energy-sensitive HEXITEC detector in the Henry Moseley X-ray Imaging Facility at The University of Manchester. The following data contains all the files necessary for reconstruction of each dataset. The biological specimens were produced as they each contain multiple contrast agents, with distinct spectral markers. When measured by an energy-sensitive detector, each contrast agent may be identified and segmented individually following spectral analysis. A mouse hindlimb was double-stained with elemental iodine and BaSO4. A mouse forelimb was triple-stained with I2KI, BaSO4 and PTA. File descriptions: Contained are two HDF5 (.h5) data files, as well as two (.txt) metadata files and a MATLAB (.mat) file. Hindlimb_scan_parameters.txt provides the full sample and detector geometry of the scan acquisition for the double-stained hindlimb. Forelimb_scan_parameters.txt provides the full sample and detector geometry of the scan acquisition for the triple-stained forelimb. DS_Mouse_hindlimb_sinogram.h5 contains the full 4D sinogram constructed following flatfield normalisation of the raw projection data for the double-stained hindlimb specimen. The 4D array contains the total number of energy channels acquired during scanning, followed by vertical and horizontal pixel number, and finally total projections angles acquired. In addition, a ring artefact reduction filter was applied. TS_Mouse_forelimb_sinogram.h5 contains the full 4D sinogram constructed following flatfield normalisation of the raw projection data for the triple-stained forelimb specimen. The 4D array contains the total number of energy channels acquired during scanning, followed by vertical and horizontal pixel number, and finally total projections angles acquired. In addition, a ring artefact reduction filter was applied. Energy_axis.mat provides a direct conversion between the energy channels, and the energies (in keV) that they correspond to, following a calibration procedure prior to scanning. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/6787593 |
| Title | Hyperspectral X-ray CT datasets of an aluminium phantom containing three metal-based powders |
| Description | General Data description: This is a set of two hyperspectral (energy-resolved) X-ray CT projection datasets of a multi-phase phantom. It was acquired in a custom-built, laboratory micro-CT scanner with an energy-sensitive HEXITEC detector in the Henry Moseley X-ray Imaging Facility at The University of Manchester. The following data contains all the files necessary for reconstruction, following two hyperspectral scans of a metal, multi-phase phantom. The phantom consists of an external aluminium cylinder, with three holes, each filled with a different metal-based powder (CeO2, ZnO, Fe). Each powder provides a unique attenuation signal, with CeO2 in particular producing a distinct spectral marker which can be measured by an energy-sensitive detector. Two identical scans were acquired, with only the exposure time per projection changed. Note: Zenodo Version 2 of this dataset contains the incorrect version of the 180s, 180 projection phantom dataset, if wishing to analyse the dataset used in the associated hyperspectral paper. This version (Version 3) contains the correct dataset from the paper. File descriptions: Contained is an image (.jpg) of the sample, along with five MATLAB (.mat) data files, as well as a single text (.txt) file. Where necessary, the files have been named to match the dataset they belong to, based on the different exposure times used for each dataset. Phantom_design_measurements.jpg contains a photograph of the physical phantom, combined with a diagram showing full sample measurements. Powder_phantom_scan_geometry.txt gives a breakdown of the full sample and detector geometry used when acquiring the raw projections for both scans. Powder_phantom_30s_30Proj_sinogram.mat contains the 4D sinogram constructed following flatfield normalisation of the raw projection data, where an exposure time of 30 s was used for each projection. The 4D array contains the total number of energy channels acquired during scanning, followed by vertical and horizontal pixel number, and finally total projections angles acquired during scanning. The total number of channels in the file is 200. Powder_phantom_180s_180Proj_sinogram.mat is the 4D sinogram for the dataset, when exposure times of 180 s were used for each projection, following flatfield normalisation. A discontinuity occurs at projection 137 due to an interruption in the scan procedure. The total number of channels in the file is 200. Energy_axis.mat provides a direct conversion between the energy channels, and the energies (in keV) that they correspond to, following a calibration procedure prior to scanning. This is the same for both datasets. FF_30s.mat contains the 4D flatfield data acquired when no sample was present, in the case of 30 s exposure times. This data was used to normalise the projection datasets, as the sinogram was constructed. The first 200 channels are included. FF_180s.mat contains the 4D flatfield data for the dataset where 180 s exposure times were used. The first 200 channels are included. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | N/A |
| URL | https://zenodo.org/record/4354815 |
| Title | Hyperspectral X-ray CT datasets of three chemical phantoms |
| Description | General Data description: The following are hyperspectral (energy-resolved) X-ray CT datasets for a set of chemical phantom samples, each containing multiple phases of an aqueous contrast agent at different concentrations. All scans were acquired with an energy-sensitive HEXITEC detector in the Henry Moseley X-ray Imaging Facility at The University of Manchester. The following data contains all the files necessary for reconstruction of each dataset. The phantom samples were produced as they each offer a distinct spectral marker which, when measured by an energy-sensitive detector, may be used as a form of calibration for spectral analysis. The phantoms were for the common contrast agents of I2KI, BaSO4 and PTA. File descriptions: Contained are four MATLAB (.mat) data files, as well as three text (.txt) metadata files. Iodine_Phantom_scan_parameters.txt provides the full sample and detector geometry of the scan acquisition for the I2KI phantom. The concentrations for the iodine phases were 25, 50, 76 and 101 mg/ml of aqueous I3- ions respectively. Barium_Phantom_scan_parameters.txt provides the full sample and detector geometry of the scan acquisition for the BaSO4 phantom. The concentrations for the BaSO4 phases were 100, 200 and 400 mg/ml of BaSO4 respectively. Tungsten_Phantom_scan_parameters.txt provides the full sample and detector geometry of the scan acquisition for the PTA phantom. The concentrations for the PTA phases were 50, 100 and 200 mg/ml of PTA respectively. Iodine_phantom_sinogram.mat contains the full 4D sinogram constructed following flatfield normalisation of the raw projection data for the I2KI phantom. The 4D array contains the total number of energy channels acquired during scanning, followed by vertical and horizontal pixel number, and finally total projections angles acquired. In addition, a ring artefact reduction filter was applied, as well as a centre-of-rotation correction. Barium_phantom_sinogram.mat contains the full 4D sinogram constructed following flatfield normalisation of the raw projection data for the BaSO4 phantom. The 4D array contains the total number of energy channels acquired during scanning, followed by vertical and horizontal pixel number, and finally total projections angles acquired. In addition, a ring artefact reduction filter was applied, as well as a centre-of-rotation correction. Tungsten_phantom_sinogram.mat contains the full 4D sinogram constructed following flatfield normalisation of the raw projection data for the PTA phantom. The 4D array contains the total number of energy channels acquired during scanning, followed by vertical and horizontal pixel number, and finally total projections angles acquired. In addition, a ring artefact reduction filter was applied, as well as a centre-of-rotation correction. Energy_axis.mat provides a direct conversion between the energy channels, and the energies (in keV) that they correspond to, following a calibration procedure prior to scanning. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/6787488 |
| Title | Neutron tomography data of high-purity metal rods using golden-ratio angular acquisition (IMAT, ISIS) |
| Description | General description: This is a neutron tomography projection data set acquired at the IMAT beamline of the ISIS Neutron and Muon Source, Harwell, UK. It was acquired using a 512-by-512 pixel MCP time-of-flight detector (pixel size 0.055 mm) binned into 2332 energy intervals between 1.7Å and 5.5Å using a parallel-beam scan geometry. 186 projections, each with 30 min exposure time (20 micro A), in the golden-ratio angular acquisition-mode. That is, a constant angular increment of (sqrt(5)-1)/2*180 degrees = 111.2461 degrees was used, and if an angle was outside 0 to 180 it was wrapped to that interval. Data was preprocessed to compensate for distortions caused by detector electronics and then summed over energy bins to simulate a white-beam data set. The data has not been corrected for centre-of-rotation offset. This can be achieved for example by cropping 52 pixels off all images from the left. The sample was an Al cylinder (Ø 22mm) with cylindrical inset holes drilled from the top: A central 10mm hole (left empty) and 5 holes of 3mm in pentagon corner positions and 5 holes of 1mm in pentagon corner positions offset from the 3mm set. High-purity elemental Cu, Fe, Ni, Ti, and Zn were inserted in the 3mm and 1mm holes with a single 1mm hole left empty. File descriptions: The data consists of a single ZIP file with the following contents: 186 TIFF files - these are the individual projection images. golden_ratio_angles.txt - this text file lists the 186 angles in degrees at which the projections were acquired. scan_parameters.txt - this text file contains geometric metadata about the experimental scan configuration. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | Impact not yet realised |
| URL | https://zenodo.org/record/4273968 |
| Title | Neutron tomography data of high-purity metal rods using golden-ratio angular acquisition (IMAT, ISIS) |
| Description | This is a neutron tomography projection data set acquired at the IMAT beamline of the ISIS Neutron and Muon Source, Harwell, UK. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | N/A |
| URL | https://zenodo.org/record/4273969#.ZA8jsnbP0uV |
| Title | Universal Test data set for algorithmic development |
| Description | SophiaBeads Dataset are acquired specifically for testing and comparing reconstruction methods for x-ray computed tomography. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | None to date |
| URL | https://zenodo.org/record/16474#.WKbnVctvgy8 |
| Description | Collaboration with Dr Vitor Hugo Carmeiro |
| Organisation | University of Minho |
| Country | Portugal |
| Sector | Academic/University |
| PI Contribution | Use of facilities and knowledge |
| Collaborator Contribution | Performed collaborative research aimed at characterising composite materials using Computed Tomography |
| Impact | A number of papers are in preparation |
| Start Year | 2020 |
| Description | Collaboration with Professor Shengchuan Wu |
| Organisation | Southwest Jiaotong University |
| Country | China |
| Sector | Academic/University |
| PI Contribution | Use of facilities and knowledge |
| Collaborator Contribution | Carried out experiments to assess the fatigue and fracture damage mechanisms of 3D printed or laser welded lightweight materials (high strength Al alloys and Ti alloys) by using both laboratory and synchrotron high-resolution micro computed tomography |
| Impact | A number of papers are in preparation |
| Start Year | 2018 |
| Title | Anaconda of the Python software CIL |
| Description | Good software development practices have been implemented, including software code project management, version control, issue tracking, and systematic code testing and builds. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Impact | We have made public releases through Anaconda of the Python software CIL. |
| URL | http://cil.readthedocs.io/en/latest/ |
| Title | Code to reproduce results of "Core Imaging Library Part I: a versatile python framework for tomographic imaging" |
| Description | This code reproduces all the results presented in the article Core Imaging Library Part I: a versatile python framework for tomographic imaging by Jakob S. Jørgensen, Evelina Ametova, Genoveva Burca, Gemma Fardell, Evangelos Papoutsellis, Edoardo Pasca, Kris Thielemans, Martin Turner, Ryan Warr, William R. B. Lionheart, and Philip J. Withers which will be available from 5 July 2021 at https://doi.org/10.1098/rsta.2020.0192 A preprint is available from arXiv: https://arxiv.org/abs/2102.04560 Instructions are available in the file README.md as well as at the source GitHub repository https://github.com/TomographicImaging/Paper-2021-RSTA-CIL-Part-I |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Impact | This has grown to be used in many institutions across the UK, Europe and the US, many collaborations formed including with the ISIS neutron facility, EPAC laser facility. |
| URL | https://zenodo.org/record/4744394 |
| Title | Code to reproduce results of "Core Imaging Library Part II: multichannel reconstruction for dynamic and spectral tomography" |
| Description | This code reproduces all the results presented in the article Core Imaging Library Part II: multichannel reconstruction for dynamic and spectral tomography by Evangelos Papoutsellis, Evelina Ametova, Claire Delplancke, Gemma Fardell, Jakob S. Jørgensen, Edoardo Pasca, Martin Turner, Ryan Warr, William R. B. Lionheart, and Philip J. Withers which will be available from 5 July 2021 at https://doi.org/10.1098/rsta.2020.0193 A preprint is available from arXiv: https://arxiv.org/abs/2102.06126 Instructions are available in the file README.md as well as at the source GitHub repository https://github.com/TomographicImaging/Paper-2021-RSTA-CIL-Part-II |
| Type Of Technology | Software |
| Year Produced | 2021 |
| URL | https://zenodo.org/record/4744745 |
| Title | Iterative Tomographic Reconstruction code |
| Description | This project focuses on hardware acceleration of conventional and novel iterative reconstruction techniques for computed tomography. The idea is to develop software which will be highly effective for parallel beam reconstruction in limited and missing wedge problems. The software includes (restricted access for developes): •Projection-backprojection routines for parallel, fan beam geometry •Various iterative reconstruction modules: Landweber, CGLS, MLEM, OSEM, FISTA, Primal-Dual •Various regularisation procedures: Tikhonov-L2, TV-L1, Diffusion, Higher order PDEs, Non-local means, Patch-based penalties •Novel spatial-temporal regularisation techniques •Novel structurual priors for hybrid reconstruction •Real data reconstruction routines, artifacts removal |
| Type Of Technology | Software |
| Year Produced | 2015 |
| Impact | It has been downloaded 2858 times |
| URL | https://ccpforge.cse.rl.ac.uk/gf/project/ccpi_itr/ |
| Title | Quantification code for tomography |
| Description | The plug-ins available at the moment are: •3D quantification - calculates various quantities from labelled 3D image, including particle size, PCA analysis and fitted surface data. •Connected components - can be used to label the separate components in a binary image. •Accessibe volume - calculate the accessible volume distribution for a 3D scaffold.(http://dx.doi.org/10.1016/j.jmatprotec.2014.05.006) •Nexus Reader - Nexus reader to read Diamond Light Source data into image analysis software. |
| Type Of Technology | Software |
| Year Produced | 2015 |
| Impact | Downloaded 3317 times |
| URL | https://ccpforge.cse.rl.ac.uk/gf/project/iqa/ |
| Title | The Core Imaging Library |
| Description | CIL is an open-source mainly Python framework for tomographic imaging for cone and parallel beam geometries. It comes with tools for loading, preprocessing, reconstructing and visualising tomographic data. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | This has grown to be used in many institutions across the UK, Europe and the US, many collaborations formed including with the ISIS neutron facility, EPAC laser facility. |
| Description | 1-day training school for the Core Imaging Library |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Overview of the Core Imaging Library and how it can be used. 33 attendees |
| Year(s) Of Engagement Activity | 2021 |
| Description | 12th annual Tomography for Scientific Advancement (ToScA) symposium |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Team member gave presentation at virtual conference |
| Year(s) Of Engagement Activity | 2021 |
| Description | A specialist workshop on 'fibre reinforced composites' |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | 34 UK researchers and technicians attended a specialist workshop on 'fibre reinforced composites' at Royce Institute on knowledge exchange. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Advanced X-ray Imaging Workshop and Fringe Meeting (14-15 June 2018, organised by DLS / MDC); |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Advanced X-ray Imaging Workshop and Fringe Meeting (14-15 June 2018, organised by DLS / MDC); Attendance 19, CCPi hosted one-day Fringe event for UK researchers and Technicians: at STFC national facilities |
| Year(s) Of Engagement Activity | 2018 |
| Description | Analysis Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Workshop on digital volume correlation (DVC) analysis, outlining state of the art and applications in materials science. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Avizo courses at UoM |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | 3 groups of 14 UK researchers and technicians attended Avizo courses at UoM (6-7 March 2018, 5-6 June 2018, 28-29 November 2018) which was held at the Royce Institute. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Avizo visualisation hands-on session at RAL |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | 8 UK researchers and technicians attended an Avizo visualisation hands-on session at RAL (17 May 2018) at STFC national facilities. |
| Year(s) Of Engagement Activity | 2018 |
| Description | CCPi Virtual Seminar Series |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Seminar series over zoom in which researchers and industry discussed how they used the Core Imaging Library. There were over 25 events covering a total of 369 attendees with 45 speakers. |
| Year(s) Of Engagement Activity | 2020,2021 |
| Description | CCPi Working Group event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Discussion with SPIERS looking software product range |
| Year(s) Of Engagement Activity | 2021 |
| Description | CCPi sponsored food and drink; IBFEM-4i at Swansea (3-4 [training] and 5-6 [users' workshop] September 2018) |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | CCPi sponsored food and drink; IBFEM-4i at Swansea (3-4 [training] and 5-6 [users' workshop] September 2018) - Attendance 25 training and 37 workshop; for UK researchers |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://ibfem.co.uk/2018/ |
| Description | CIL @ ToScA UK & Europe 2022, Queen Mary University London, 7 - 9 September |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | We present the Core Imaging Library (CIL) - a versatile open-source Python package for tomographic imaging reconstruction and analysis. CIL can be used for the entire tomography data workflow from loading common lab and synchrotron X-ray CT data formats, pre-processing for various imperfections, reconstruction by filtered back-projection or a variety of iterative methods as well as data visualisation and exploration. CIL offers tools for conventional as well as challenging setups including in-situ experiments with imaging rigs, fast dynamic CT, hyper-spectral CT, and non-standard scan geometries such as laminography. In this talk, we give an overview of the functionality provided by CIL and provide multiple application examples, including comparisons of filtered back-projection reconstruction with emerging iterative reconstruction methods. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.ccpi.ac.uk/CIL |
| Description | CIL Training @ ToScA UK 2021 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Hands-on training for the Core Imaging Library (CIL), an open-source reconstruction platform for challenging and novel data. |
| Year(s) Of Engagement Activity | 2021 |
| Description | CIL Training Course @ IBSim 18 October 2022 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Session 1: Introduction to XCT and the CIL framework for reconstruction of commercial lab-based XCT data with FBP/FDK Session 2: Pre-processing of XCT data, e.g. centre of rotation correction Session 3: Iterative reconstruction methods for standard XCT data Session 4 (choose one of): Reconstruction of data simulated from gVXR Advanced iterative reconstruction with spectral XCT data Advanced iterative reconstruction on laminography XCT data |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://ibsim.co.uk/events/ibsim-4i/registration/ |
| Description | CT image based modelling of composite materials' failure |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | An invited lecture to an international conference. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Course at Manchester DVC (Digital Volume Correlation) by Kamel Madi (Thermo Scientific™ Amira-Avizo) |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Attendance 10, funded trainers for course from CCPi, held at Royce Institute: UK researchers and technicians |
| Year(s) Of Engagement Activity | 2018 |
| Description | Dataset training |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | A training course was held over two days at Harwell Campus to help users with the Visualisation & quantification of tomographic datasets |
| Year(s) Of Engagement Activity | 2021 |
| Description | Digital Volume Correlation. Training on iDVC |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Digital volume correlation (DVC) is used in material science to quantify the internal displacements and strain fields from in situ tomography experiments. This workshop will cover the theory of in situ tomography experiments and DVC analysis, followed by a practical session using the Collaborative Computational Project in Tomographic Imaging (CCPi) iDVC app. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Dimensional XCT conference (2-3 July 2018, organised by NPL); and ToScA Symposium (10-12 September 2018, organised by RMS). |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Dimensional XCT conference (2-3 July 2018, organised by NPL); and ToScA Symposium (10-12 September 2018, organised by RMS). CCPi had an exhibition stand and supported events for UK and international researchers: visitor footfall ~70 + ~80 |
| Year(s) Of Engagement Activity | 2018 |
| Description | Fully3D Training School for the Synergistic Image Reconstruction Framework (SIRF) and Core Imaging Library (CIL) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was an online training course for the image reconstruction, optimisation and regularisation software packages: Synergistic Image Reconstruction Framework (SIRF) and the Core Imaging Library (CIL). |
| Year(s) Of Engagement Activity | 2021 |
| Description | Hackathon |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | A hackathon took place at STFC to develop an algorithms benchmark for tomographic image reconstruction |
| Year(s) Of Engagement Activity | 2021 |
| Description | IBSim-4i (Image-Based Simulation for Industry) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Team member gave presentation at virtual conference |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://ibfem.co.uk/events/ |
| Description | Interview, P D Lee, by CGTN Europe for RAZOR programme. |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | P D Lee was interviewed by S Somara from CGTN Europe for RAZOR TV prgogramme, topics include 3D printing for aerospace industry and volcano programme. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Invited Talk, ToScA UK and Europe 2019, Sept 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Kamel Madi et al. was invited to give a talk at the ToScA UK and Europe 2019 on "Digital Volume Correlation (DVC)" |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.toscainternational.org/ |
| Description | Invited talk, P D Lee, Walsh, et al, Institute of Healthcare Engineering Colloquium |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | P D Lee gave a presentation entitled "The Human Organ Project using the ESRF-EBS" at Institute of Healthcare Engineering Colloquium |
| Year(s) Of Engagement Activity | 2020 |
| Description | Invited talk, PD Lee, History of X-ray Imaging of Materials |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | PD Lee gave an invited talk entittled "History of X-ray Imaging of Materials" at the in situ X-ray imaging: applications from aerospace to biotechnology workshop |
| Year(s) Of Engagement Activity | 2021 |
| Description | Invited talk, PD Lee, Imaging of Additive Manufacturing |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | PD Lee gave an invited talk entittled "Imaging of Additive Manufacturing " at the in situ X-ray imaging: applications from aerospace to biotechnology workshop |
| Year(s) Of Engagement Activity | 2021 |
| Description | Invited talk, PD Lee/RT, Bio applications - Covid case study |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | PD Lee gave an invited talk entitled "Bio applications - Covid case study" at the in situ X-ray imaging: applications from aerospace to biotechnology workshop |
| Year(s) Of Engagement Activity | 2021 |
| Description | Keynote, ICASP-5 and CSSCR-5, June 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Peter D. Lee was invited to give a keynote presentation at the 5th International Conference on Advances in Solidification Process (ICASP-5) and 5th International Symposium on Cutting Edge of Computer Simulation of Solidification, Casting and Refining (CSSCR-5) on "Capturing rapid solidification during laser additive manufacturing using synchrotron imaging" |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.icasp5-csscr5.org/ |
| Description | Keynote, plenary talk, P D Lee, Technical University of Denmark |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | P D Lee gave a keynote plenary presentation entitled "Seeing Materials Through a Synchrotron Looking Glass: Inside Additive Manufacturing to Intact Covid-19 Injured Organs with Micron Resolution" at Technical University of Denmark |
| Year(s) Of Engagement Activity | 2020 |
| Description | Lunch-and-learn virtual seminar series |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A series of weekly virtual seminars with invited speakers. |
| Year(s) Of Engagement Activity | 2020,2021 |
| Description | Member, STFC Scientific Advisory Board Meeting, Feb 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Professor Peter D Lee invited to be a member of the Scientific Advisory Board of the STFC Annual Meeting |
| Year(s) Of Engagement Activity | 2019 |
| Description | Monthly Lunch-and-Learn sessions (Royce Institute) and software-show-tell events at RAL (Harwell Campus). |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | - Monthly Lunch-and-Learn sessions (Royce Institute) and software-show-tell events at RAL (Harwell Campus). In 2018 for local knowledge exchange ... ... there were 11 meetings at Royce Institute, (total attendance 226 - two using video conferencing). ... there were 6 meetings at STFC national facilities (total attendance ~49) ... and 1 meeting at UoM Mathematics department (total attendance 11) |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://tyne.dl.ac.uk/twiki/bin/view/Visualisation/VisSeminars |
| Description | Network t-conf meetings |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Network t-conf meetings occur continually, with updated website, and regular newsletters, comprises talks and training events. The size of our community has risen from ~250 in 2013 to over 400 by the end of 2018; over 60% growth. |
| Year(s) Of Engagement Activity | 2013,2014,2015,2016,2017,2018 |
| Description | Online Training - Introduction to the Core Imaging Library (CIL) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This short training course will introduce you to using CIL for pre-processing and reconstruction of tomographic data. You will be introduced to iterative reconstruction algorithms and compare these with the typical FBP/FDK reconstructions. The course will be held remotely. The training material will be provided for you through the STFC cloud which you will access through a browser. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Online Training - Introduction to the Core Imaging Library (CIL) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This short training course will introduce you to using CIL for pre-processing and reconstruction of tomographic data. You will be introduced to iterative reconstruction algorithms and compare these with the typical FBP/FDK reconstructions. The course will be held remotely. The training material will be provided for you through the STFC cloud which you will access through a browser. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Organiser, ImagingBioPro Workshop "Learning How Large Facilities Can Help Image Musculoskeletal (MSK) Processes", at Diamond Light Source, Sept 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Marta Godinho organised the ImagingBioPro Workshop "Learning How Large Facilities Can Help Image Musculoskeletal (MSK) Processes" at Diamond Light Source |
| Year(s) Of Engagement Activity | 2019 |
| Description | Parmesh Gajjar to USA, England and Wales on Nikon hacking training/code. |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Parmesh Gajjar to USA, England and Wales on Nikon hacking training/code. Publicity at lunch-and-learn (accounted for above) and funded training session at Swansea (attendance 5) - UK technicians. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Publication highlight, K Madi, K A Staines, B K Bay, B Javaheri, H Geng, A J Bodey, S Cartmell, A A Pitsillides, P D Lee, in Diamond Annual Review 2019/20 |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | "K Madi, K A Staines, B K Bay, B Javaheri, H Geng, A J Bodey, S Cartmell, A A Pitsillides, P D Lee, In situ characterisation of nanoscale strains in loaded whole joints via synchrotron X-ray tomography. Nat. Biomed. Eng. 4, 343 (2020). DOI: 10.1038/s41551-019-0477-1" was highlighted in Diamond Annual Review 2019/20 |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.diamond.ac.uk/docroot/flippingbooks/DiamondAnnualReview2020/ |
| Description | Publication highlight, K Madi, K A Staines, B K Bay, B Javaheri, H Geng, A J Bodey, S Cartmell, A A Pitsillides, P D Lee, in F1000Prime |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | "K Madi, K A Staines, B K Bay, B Javaheri, H Geng, A J Bodey, S Cartmell, A A Pitsillides, P D Lee, In situ characterisation of nanoscale strains in loaded whole joints via synchrotron X-ray tomography. Nat. Biomed. Eng. 4, 343 (2020). DOI: 10.1038/s41551-019-0477-1" was recommended in F1000Prime as being of special significance in its field by F1000 Faculty Member Peter Torzilli. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Publication highlight, K Madi, K A Staines, B K Bay, B Javaheri, H Geng, A J Bodey, S Cartmell, A A Pitsillides, P D Lee, in Nature Biomedical Engineering |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | "K Madi, K A Staines, B K Bay, B Javaheri, H Geng, A J Bodey, S Cartmell, A A Pitsillides, P D Lee, In situ characterisation of nanoscale strains in loaded whole joints via synchrotron X-ray tomography. Nat. Biomed. Eng. 4, 343 (2020). DOI: 10.1038/s41551-019-0477-1" was highlighted in Nature Biomedical Engineering. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Royal Society Satelitte Exhibition |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | This exhibit showed how we've used 4D synchrotron X-ray tomography of magma to better understand volcanic eruptions, and of ice crystals, to work out why some ice cream tastes better! This was a repeat of the summer exhibition held outside London as part of Manchester Science Festival, nearly 13, 000 visitors came over the 5 day exhibition |
| Year(s) Of Engagement Activity | 2016 |
| URL | https://royalsociety.org/science-events-and-lectures/science-exhibition-manchester/ |
| Description | Royal Society Summer Exhibition |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Entitled "4D Science" this exhibit showed how we've used 4D synchrotron X-ray tomography of magma to better understand volcanic eruptions, and of ice crystals, to work out why some ice cream tastes better. 16,000 visitors came to the week long exhibition. |
| Year(s) Of Engagement Activity | 2016 |
| URL | https://royalsociety.org/science-events-and-lectures/summer-science-exhibition/exhibits/4d-science/ |
| Description | SMI Hub Workshop: It's not Easy Being Green - Sustainability, Plastics and Your Business 2023 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | Sustainability workshop for SMEs in the Greater Manchester area |
| Year(s) Of Engagement Activity | 2022,2023 |
| Description | Talk at IBSim-4i 2021 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Gave a talk on the CIL at IBSim-4i 2021 to promote the resource to a wider audience |
| Year(s) Of Engagement Activity | 2021 |
| Description | Talk at the CoSeC Annual Conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | A talk was given at the CoSeC annual conference entitled "The CCPi core imaging library, a versatile software for tomographic imaging", which helped to raise the profile of the resource. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.scd.stfc.ac.uk/Pages/CIUK-2021-Breakout-Sessions.aspx |
| Description | Talk, "For the love of engineering show - feature a unique blend of short films, music, science comedy and engineering research", UCL, Oct 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Peter D Lee & Le Gall gave a presentation of the research carried out in our group to the general public in a London West End Theatre |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://mecheng.ucl.ac.uk/events/for-the-love-of-engineering/ |
| Description | Talk, "Learning How Large Facilities Can Help Image Musculoskeletal (MSK) Processes" IBP Workshop at Harwell |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Himadri Gupta gave a talk at the IBP workshop "Learning How Large Facilities Can Help Image Musculoskeletal (MSK) Processes" |
| Year(s) Of Engagement Activity | 2019 |
| Description | Talk, Departmental Seminar at the Department of Engineering, University of Oxford |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Himadri S. Gupta gave a seminar in the Solid Mechanics & Materials Engineering Group seminar series, University of Oxford, Oxford on "Illuminating the nanomechanics of hierarchical biological composites: Insights from in-situ synchrotron X-ray techniques". |
| Year(s) Of Engagement Activity | 2019 |
| Description | Talk, ImagingBioPro Workshop "Learning How Large Facilities Can Help Image Musculoskeletal (MSK) Processes" at Diamond Light Source, Sept 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Professor Peter D Lee gave a talk at the ImagingBioPro workshop "Learning How Large Facilities Can Help Image Musculoskeletal (MSK) Processes" |
| Year(s) Of Engagement Activity | 2019 |
| Description | Training Course |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Avizo Course at University of Manchester designed to guide beginners on how to use the programme. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Training Course at Conference |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Three week training course prior to the 16th International Meeting on Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine. The course covered image reconstruction for PET, MRI and x-ray CT, emphasising commonalities but allowing participants to concentrate on topics that fit their interest. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Training at conference |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Training day on reconstruction toolbox which increased understanding of software. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.npl.co.uk/research/dimensional/dxct-conference/dxct-conference-2021 |
| Description | Training school at PSMR2022 - Total body PET workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Workshop and training session for CIL |
| Year(s) Of Engagement Activity | 2022 |
| Description | Training session at conference |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Provided two 3hr hands-on CIL training sessions at the 2021 ToScA Europe conference, which led to an increased understanding of how to use the software |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.toscainternational.org |
| Description | UK Research and Innovation Launch Event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | PDL Participated in UK Research and Innovation (implementing policy) |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://blogs.bl.uk/living-knowledge/2018/05/uk-research-and-innovation-launched-at-the-british-libr... |
| Description | UKRI Research Infrastructure Roadmap Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | PDL Participated in UKRI Research Infrastructure Roadmap Workshop (implementing policy) on 14 June |
| Year(s) Of Engagement Activity | 2018 |
| Description | World Cup trophy |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | To coincide with the 50th anniversary of England winning the World Cup we linked with the National Football Museum in Manchester to scan the Jules Rimet trophy. The story was picked up by local news, MEN, ITV and Wired UK |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.manchester.ac.uk/discover/news/manchester-scientists-solve-trophy-mystery/ |