Tomographic Imaging: UK Collaborative Computational Projects
Lead Research Organisation:
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. Critical to the CT process is a pipeline of computer algorithms carrying out an interdependent sequence of tasks to extract the desired information from the raw data:
i) correction and calibration starting from initial image capture,
ii) reconstruction of a 3D image from these 2D projections,
iii) analysis and quantification of features in the 3D image, and
iv) 2D and 3D visualization and animation of the 3D image and extracted features.
While the techniques are rapidly growing in popularity, most users have fairly limited options when trying to recover the 3D image. They can either use black-box software tools provided by X-ray CT instrument manufacturers, or at best, write only fairly primitive computer programs to extract key features from the images. Large, mid-range and small CT facilities across the UK represent multi million pound investments of which the full return is not realised due to unmet method and software needs. Furthermore, best practices for data analysis and application of novel computational methods are yet not routinely shared across the community adding further barrier to reaching the full potential. There is a clear need improved software tools for extracting information from CT data, as well as for strengthening collaboration across and upskilling the CT community as a whole in terms of computational methods and software.
The CCPi aims to address both of these issues. Firstly, the CCPi seeks to provide fully open-source software covering the full tomographic imaging pipeline including pre-processing and calibration, a variety of reconstruction algorithms for different forms of challenging data, artefact reduction codes, and image analysis procedures. The collection of tools released under the name Core Imaging Library (CIL) caters for inexperienced users by easy-to-use standard algorithms, as well as giving expert users full flexibility to construct bespoke data processing pipelines. Secondly, the CCPi seeks to strengthen and grow the UK CT community through networking activities, staff exchanges, training and seminars. The activities will continue to connect a highly multi-disciplinary community of mathematicians, physicists, engineers, instrument scientists, researchers in the applied sciences (users) as well as industry and cultural heritage groups.
i) correction and calibration starting from initial image capture,
ii) reconstruction of a 3D image from these 2D projections,
iii) analysis and quantification of features in the 3D image, and
iv) 2D and 3D visualization and animation of the 3D image and extracted features.
While the techniques are rapidly growing in popularity, most users have fairly limited options when trying to recover the 3D image. They can either use black-box software tools provided by X-ray CT instrument manufacturers, or at best, write only fairly primitive computer programs to extract key features from the images. Large, mid-range and small CT facilities across the UK represent multi million pound investments of which the full return is not realised due to unmet method and software needs. Furthermore, best practices for data analysis and application of novel computational methods are yet not routinely shared across the community adding further barrier to reaching the full potential. There is a clear need improved software tools for extracting information from CT data, as well as for strengthening collaboration across and upskilling the CT community as a whole in terms of computational methods and software.
The CCPi aims to address both of these issues. Firstly, the CCPi seeks to provide fully open-source software covering the full tomographic imaging pipeline including pre-processing and calibration, a variety of reconstruction algorithms for different forms of challenging data, artefact reduction codes, and image analysis procedures. The collection of tools released under the name Core Imaging Library (CIL) caters for inexperienced users by easy-to-use standard algorithms, as well as giving expert users full flexibility to construct bespoke data processing pipelines. Secondly, the CCPi seeks to strengthen and grow the UK CT community through networking activities, staff exchanges, training and seminars. The activities will continue to connect a highly multi-disciplinary community of mathematicians, physicists, engineers, instrument scientists, researchers in the applied sciences (users) as well as industry and cultural heritage groups.
Planned Impact
Economy
X-ray imaging is already well established in the security, non-destructive evaluation and health industries with 100,000 plus scanners worldwide. Increasingly CT is seen as a way of helping to develop new products, especially in the additive manufacturing area where identifying internal defects are critical, but also in many other areas where the relationship between manufacturing processes and part integrity is important, particularly for high value and safety critical components. We already have over 40 industrialists engaged in our CCP network including key UK based partners. Much of our funding is aimed at developing impact pathways to ensure that both the X-ray systems at facilities such as the large scale facilities, the newly established mid-scale National Research Facility and individual facilities are able to answer questions of key economic importance through the exploitation of new software and algorithms.
In the last phase industrial attendees have attended, presented and exhibited at our events to gain feedback, link up with users and in some cases to incorporate tools we have developed for their users.
With a work programme focused on workflows and industrial applications in CCPi's Phase III, industry will also have an increasing role on the Working Group to identify key issues from their perspective prior to developing the framework. As the CCP continues to develop it will broaden its remit into other tomographic applications (already incorporating code links with PET, MRI and Neutron Tomography) making this industrial focussed community larger and more important.
Knowledge
This CCPi will benefit; Diamond Light Source x-ray imaging users, ISIS Neutron and Muon spallation users, CLF laser-induced x-ray and those with access to laboratory and shared EPSRC strategic x-ray facilities.
People
The EPSRC Software Infrastructure Strategy 2018 identifies "people" as one its five key objectives. Three of the work program leads are early-career academics. The CCPi network will continue to upskill members within the community and has a strong record of developing young and mature researchers, both within the specific research groups and across the CCPi network. So far, in Phase II of the CCPi, there have been over 350 attending training courses; each year over 300 attend the three tomography-week events; 510 attendees at the 56 monthly seminars and a growing 400 email opt-in list. We have supported two spin-out companies and three members of the Working Group have been promoted to professors.
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 EPSRC Tier 2 regions. Following the mantra "Better Software Better Research" we have members who have fellowships within the SSI (Software Sustainability Institute), the ATI (Alan Turing Institute); and work closely with the newly formed RSE (Research Software Engineering) Society. We are also aware of the further overlaps with proposed CCPs including; CCP PET/MR, and CCP EM; and components of the code is being developed through projects with the Ada Lovelace Centre, Royce Institute and Alan Turing Institute.
Internationally we have representation and collaboration with Europe and have new links with Kitware Inc (TomViz and Paraview, Marcus Hanwell) and Oregon State University (DCV library, Brian Bay).
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. In the last Phase CCP code was involved in two Royal Society Exhibitions, the Cheltenham Science Festival and numerous open and outreach days - 13,750 visitors passed through the exhibition site at the Festival.
X-ray imaging is already well established in the security, non-destructive evaluation and health industries with 100,000 plus scanners worldwide. Increasingly CT is seen as a way of helping to develop new products, especially in the additive manufacturing area where identifying internal defects are critical, but also in many other areas where the relationship between manufacturing processes and part integrity is important, particularly for high value and safety critical components. We already have over 40 industrialists engaged in our CCP network including key UK based partners. Much of our funding is aimed at developing impact pathways to ensure that both the X-ray systems at facilities such as the large scale facilities, the newly established mid-scale National Research Facility and individual facilities are able to answer questions of key economic importance through the exploitation of new software and algorithms.
In the last phase industrial attendees have attended, presented and exhibited at our events to gain feedback, link up with users and in some cases to incorporate tools we have developed for their users.
With a work programme focused on workflows and industrial applications in CCPi's Phase III, industry will also have an increasing role on the Working Group to identify key issues from their perspective prior to developing the framework. As the CCP continues to develop it will broaden its remit into other tomographic applications (already incorporating code links with PET, MRI and Neutron Tomography) making this industrial focussed community larger and more important.
Knowledge
This CCPi will benefit; Diamond Light Source x-ray imaging users, ISIS Neutron and Muon spallation users, CLF laser-induced x-ray and those with access to laboratory and shared EPSRC strategic x-ray facilities.
People
The EPSRC Software Infrastructure Strategy 2018 identifies "people" as one its five key objectives. Three of the work program leads are early-career academics. The CCPi network will continue to upskill members within the community and has a strong record of developing young and mature researchers, both within the specific research groups and across the CCPi network. So far, in Phase II of the CCPi, there have been over 350 attending training courses; each year over 300 attend the three tomography-week events; 510 attendees at the 56 monthly seminars and a growing 400 email opt-in list. We have supported two spin-out companies and three members of the Working Group have been promoted to professors.
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 EPSRC Tier 2 regions. Following the mantra "Better Software Better Research" we have members who have fellowships within the SSI (Software Sustainability Institute), the ATI (Alan Turing Institute); and work closely with the newly formed RSE (Research Software Engineering) Society. We are also aware of the further overlaps with proposed CCPs including; CCP PET/MR, and CCP EM; and components of the code is being developed through projects with the Ada Lovelace Centre, Royce Institute and Alan Turing Institute.
Internationally we have representation and collaboration with Europe and have new links with Kitware Inc (TomViz and Paraview, Marcus Hanwell) and Oregon State University (DCV library, Brian Bay).
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. In the last Phase CCP code was involved in two Royal Society Exhibitions, the Cheltenham Science Festival and numerous open and outreach days - 13,750 visitors passed through the exhibition site at the Festival.
Organisations
Publications
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
Brown R
(2021)
Motion estimation and correction for simultaneous PET/MR using SIRF and CIL.
in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences
Ferrucci M
(2021)
Monte Carlo reconstruction: a concept for propagating uncertainty in computed tomography
in Measurement Science and Technology
Fogarty K
(2022)
Recovering the second moment of the strain distribution from neutron Bragg edge data
in Applied Physics Letters
Jørgensen JS
(2021)
Core Imaging Library - Part I: a versatile Python framework for tomographic imaging.
in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences
King AJ
(2022)
The Winchcombe meteorite, a unique and pristine witness from the outer solar system.
in Science advances
M Sandoval
(2021)
Multiple DOF for X-ray CT Hydrocarbon Exploration
Papoutsellis E
(2021)
Core Imaging Library - Part II: multichannel reconstruction for dynamic and spectral tomography.
in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences
Tsoumpas C
(2021)
Synergistic tomographic image reconstruction: part 1.
in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences
Tsoumpas C
(2021)
Synergistic tomographic image reconstruction: part 2.
in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences
Warr R
(2022)
Quantifying multiple stain distributions in bioimaging by hyperspectral X-ray tomography.
in Scientific reports
Warr R
(2021)
Enhanced hyperspectral tomography for bioimaging by spatiospectral reconstruction.
in Scientific reports
Description | This project has led to new software reconstruction algorithms now being widely used by the tomographic imaging community leading to better information from VCT scanning as well as a significant amount of skills training. |
Exploitation Route | The software library is openly available and being added to with help from the wider community. |
Sectors | Aerospace, Defence and Marine,Agriculture, Food and Drink,Chemicals,Construction,Creative Economy,Digital/Communication/Information Technologies (including Software),Electronics,Energy,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Culture, Heritage, Museums and Collections,Pharmaceuticals and Medical Biotechnology,Transport |
Description | Our algorithms have been used by the wider community to analyse their 3D data |
First Year Of Impact | 2022 |
Sector | Aerospace, Defence and Marine,Agriculture, Food and Drink,Chemicals,Construction,Creative Economy,Digital/Communication/Information Technologies (including Software),Electronics,Energy,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Culture, Heritage, Museums and Collections,Pharmaceuticals and Medical Biotechnology,Transport |
Impact Types | Cultural |
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 Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | n/a |
URL | https://zenodo.org/record/4744745 |
Title | Core Imaging Library - Part I: a versatile Python framework for tomographic imaging |
Description | We present the Core Imaging Library (CIL), an open-source Python framework for tomographic imaging with particular emphasis on reconstruction of challenging datasets. Conventional filtered back-projection reconstruction tends to be insufficient for highly noisy, incomplete, non-standard or multi-channel data arising for example in dynamic, spectral and in situ tomography. CIL provides an extensive modular optimization framework for prototyping reconstruction methods including sparsity and total variation regularization, as well as tools for loading, preprocessing and visualizing tomographic data. The capabilities of CIL are demonstrated on a synchrotron example dataset and three challenging cases spanning golden-ratio neutron tomography, cone-beam X-ray laminography and positron emission tomography. |
Type Of Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | Not yet noticed |
URL | https://publikationen.bibliothek.kit.edu/1000136787 |
Title | Duke Spleen Data Set |
Description | CT and MRI images with associated binary spleen segmentation masks; includes axial and coronal images, MRI includes SSFSE and T1w opposed phase contrasts; includes a range of normal and abnormal spleen sizes and shapes in the setting of chronic liver disease. |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | CT and MRI images with associated binary spleen segmentation masks; includes axial and coronal images, MRI includes SSFSE and T1w opposed phase contrasts; includes a range of normal and abnormal spleen sizes and shapes in the setting of chronic liver disease. |
URL | https://zenodo.org/record/7636640 |
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 |
Impact | n/a |
URL | https://zenodo.org/record/7363345 |
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 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 | 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 | 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. |
Title | Working with The Core Imaging Library (CIL) on developing open-source python-based reconstruction pipelines for all users at UK doing X-ray tomography. |
Description | Developing open-source python-based reconstruction pipelines for all users at UK doing x-ray tomography. |
Type Of Technology | Webtool/Application |
Year Produced | 2023 |
Open Source License? | Yes |
Impact | Impact not realised yet. |
URL | https://ccpi.ac.uk/cil/ |
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 | 6th dimensional x-ray computed tomography conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Attendance/talk at 6th dimensional x-ray computed tomography conference |
Year(s) Of Engagement Activity | 2022 |
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 | 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 | 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 | Conference - Rich and Nonlinear Tomography - a multidisciplinary approach |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Secured a prestigious INI (Isaac Newton Institute at Cambridge) 6 month conference slot 4 January 2023 - 30 June 2023 on RNT Rich and Nonlinear Tomography - a multidisciplinary approach [9 organisers, 9 key speakers, 70 participants] |
Year(s) Of Engagement Activity | 2023 |
URL | http://www.newton.ac.uk |
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 | 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 | 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 | 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 | The Power of Materials Modelling for Industrial Applications workshop 2022 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Workshop is organized to share knowledge and awareness of the materials modelling endeavours supported by CCP5 that are of benefit to UK PLC |
Year(s) Of Engagement Activity | 2022 |
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 |