Tomo-SAXS: Imaging full-field molecular-to-macroscale biophysics of fibrous tissues
Lead Research Organisation:
Diamond Light Source
Department Name: Science Division
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Organisations
Publications
Badar W
(2024)
Nonlinear Stress-Induced Transformations in Collagen Fibrillar Organization, Disorder and Strain Mechanisms in the Bone-Cartilage Unit
in Advanced Science
Badar W
(2022)
Collagen pre-strain discontinuity at the bone-Cartilage interface.
in PloS one
Barbieri E
(2023)
Is Stress Relaxation in Sea Cucumber Dermis Chemoelastic?
in Marine Drugs
Chen Y
(2024)
Accelerating the remodeling of collagen in cutaneous full-thickness wound using FIR soldering technology with bio-targeting nanocomposites hydrogel
in Journal of Biophotonics
Disney CM
(2023)
Image quality and scan time optimisation for in situ phase contrast x-ray tomography of the intervertebral disc.
in Journal of the mechanical behavior of biomedical materials
Heyraud A
(2024)
Calcium sources can increase mechanical properties of 3D printed bioactive hybrid bone scaffolds.
in RSC advances
Zhang Y
(2022)
Investigating the Fibrillar Ultrastructure and Mechanics in Keloid Scars Using In Situ Synchrotron X-ray Nanomechanical Imaging.
in Materials (Basel, Switzerland)
| Description | To enable the TomoSAXS platform to benefit the bioengineering community, the grant proposed to make the hardware and software available at Diamond Light Source; the current status is: Hardware: Integration of a bespoke CT-SAXS biomechanical test setup to apply TomoSAXS, which allows multiaxial rotations (with nanometre precision and in controlled hydration) is proceeding using the successful P2R design developed by co-I Peter Lee's group. The integration led by co-I Nick Terrill, beamline scientist Paul Wady and Diamond Light Source's motion- and controls group, as part of a commitment by DLS to support the TomoSAXS project. Currently, motor- and load-cell control has been established, with the sample humidity being optimised. The estimated timescale for commissioning and making available the rig is by mid-end 2025, and we intend to hold a workshop at DLS to demonstrate the method in parallel. Software: The TomoSAXS codebase is being developed on GitHub (https://github.com/himadri111/saxs-docs-tutorial/ with documentation file at docs/source/How-to.rst; in process of synchronising with Diamond's GitHub repository) with the reconstruction methods described using a widely used ReadTheDocs format. The Python-based software runs on the DLS HPC cluster, and a draft guide for running the reconstruction has been written by Elis Newham (TomoSAXS PDRA) and reviewed by the team. The next steps (by mid-end 2025) are to implement a GUI integrated with the standard UI at beamlines I22(SAXS) and I13(CT) to facilitate access to users from different backgrounds. Method dissemination: Initial results of the TomoSAXS method are being publicized in the specialist community, with a recent invited talk by Dr. Newham at the TexTom workshop at Marseilles, France, attended by the leaders in the scattering tensor tomography community, which have led to plans for collaboration with Drs. Tilman Gruenewald and Marianne Liebi. Olga Shebanova also presented technical developments on I22 to enable this type of SAXS data collection at the same conference. Four abstract submissions on different aspects of the method at the European Society of Biomechanics 2025, one of the two leading world biomechanics meetings, in Zurich, for wider dissemination. The impact-pathway to human organs and larger-scale tissues, and integration with larger-level tomographic imaging is being planned via secured upcoming beamtimes in April 2025 at ESRF. Here, human IVD will be imaged using the HiP-CT (funded by CZI) followed by TomoSAXS at ID31. Successful demonstration of TomoSAXS on human tissue (going beyond the mouse and rat models in the current grant) will enable large-scale utilisation of the method for a range of human tissues and organs, leveraging the active HiP-CT Human Organ Atlas consortium developed by PDL. |
| First Year Of Impact | 2024 |
| Sector | Healthcare |
| Description | HiP-CT Imaging Hub |
| Amount | $1,750,000 (USD) |
| Funding ID | CZIF2021-006424 |
| Organisation | Chan Zuckerberg Initiative |
| Sector | Private |
| Country | United States |
| Start | 11/2021 |
| End | 10/2024 |
| Description | HiP-CT Imaging Hub Expansion |
| Amount | $5,000,000 (USD) |
| Organisation | Chan Zuckerberg Initiative |
| Sector | Private |
| Country | United States |
| Start | 12/2022 |
| End | 11/2027 |
| Title | HiP-CT Project GitHub |
| Description | This GitHub contains codes used internally within the HiP-CT project. Where possible we've made these codes public so others can read and re-use. None of the code is designed to be general purpose or scientist-facing. |
| Type Of Material | Data analysis technique |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | HiP-CT analysis pipeline. |
| URL | https://github.com/HumanOrganAtlas |
| Title | Human Organ Atlas Hub GitHub |
| Description | This GitHub contains code and metadata to help scientists use data from Human Organ Atlas Hub. |
| Type Of Material | Data analysis technique |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | Notes and guidelines on how to use data from Human Organ Atlas Hub. |
| URL | https://github.com/HumanOrganAtlas |
| Description | A Parmenter chairing at ATEM |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | A Parmenter chairing at ATEM. Session: Large-scale DIC testing, Japan |
| Year(s) Of Engagement Activity | 2023 |
| Description | A Parmenter poster at ATEM |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | A Parmenter poster at ATEM "Combining synchrotron X-ray tomography and diffraction to investigate structure and strain across the intervertebral disc-endplate soft-hard tissue boundary", Japan |
| Year(s) Of Engagement Activity | 2023 |
| Description | A Parmenter poster at RaCH The 6th Annual Workshop on Advances in X-ray Imaging: Expanding the Frontiers of Knowledge |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | A Parmenter poster at RaCH The 6th Annual Workshop on Advances in X-ray Imaging: Expanding the Frontiers of Knowledge, "Biomechanics of the intervertebral disc-endplate junction analysed using synchrotron CT and DVC", UK |
| Year(s) Of Engagement Activity | 2023 |
| Description | A Parmenter talk at ATEM |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | A Parmenter talk at ATEM "Digital volume correlation of the intervertebral disc: a multiple tissue type analysis", Japan |
| Year(s) Of Engagement Activity | 2023 |
| Description | A Parmenter talk at Biomedeng23 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | A Parmenter talk at Biomedeng23 "Biomechanics of the intervertebral disc-endplate soft-hard tissue junction analysed using synchrotron tomography and digital volume correlation ", UK |
| Year(s) Of Engagement Activity | 2023 |
| Description | A Parmenter talk at ESB 2024 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | A Parmenter talk at ESB 2024 "LINKING NANO-TO-MACROSCALE STRUCTURE AND STRAIN IN THE VERTEBRAL ENDPLATES ", UK |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://esbiomech2024.org/ |
| Description | A Parmenter talk at ESB 2024 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | A Parmenter talk at ESB 2024 "CORRELATIVE IN SITU SYNCHROTRON SAXS, WAXS, AND CT FOR THE INVESTIGATION OF STRAIN TRANSFER ACROSS THE INTERVERTEBRAL DISC HARD-SOFT TISSUE BOUNDARY", UK |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://esbiomech2024.org/ |
| Description | A Parmenter talk at UCL Engineering students Research Festival |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | A Parmenter talk at UCL Engineering students Research Festival, "Using X-Rays to Investigate the Mechanics of the Spine", UK |
| Year(s) Of Engagement Activity | 2023 |
| Description | A Parmenter talk at the Congress of the European Society of Biomechanics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | A Parmenter talk at the Congress of the European Society of Biomechanics, "Structure and mechanics of the intervertebral disc-endplate junction analysed using synchrotron CT and DVC", The Netherlands |
| Year(s) Of Engagement Activity | 2023 |
| Description | A Parmenter, poster talk at MechEng PhD Conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | A Parmenter, poster talk at MechEng PhD Conference, "Quantifying strains across the intervertebral disc-endplate junction using synchrotron CT and DVC", UK |
| Year(s) Of Engagement Activity | 2023 |
| Description | A Parmenter, talk at BioMedEng22 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | A Parmenter, talk at BioMedEng22, "Biomechanics of the vertebral endplate analysed using in situ phase-contrast synchrotron tomography and digital volume correlation", London, UK |
| Year(s) Of Engagement Activity | 2022 |
| Description | C Disney, 2022 CoSeC Impact Award |
| 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 | Media (as a channel to the public) |
| Results and Impact | C Disney was awarded the 2022 CoSeC Impact Award, 'Catherine's work is central to CCPi. The new methodology (Digital Volume Correlation) looks very promising although it is not clear whether this has yet had an impact in real world medical diagnosis.' . |
| Year(s) Of Engagement Activity | 2022 |
| Description | C Disney, Invited talk at iDICs conference. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | C Disney, Invited talk at iDICs conference, "Fibre Tracking in Soft Tissue using Synchrotron Tomography and Digital Volume Correlation", Nantes, France. |
| Year(s) Of Engagement Activity | 2021 |
| Description | C Disney, poster at BioMedEng 22. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | C Disney, poster at BioMedEng 22, Regional Collagen Fibre Kinematics of the Intervertebral Disc, London, UK |
| Year(s) Of Engagement Activity | 2022 |
| Description | E Newham talk at Biomedeng23 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | E Newham talk at Biomedeng 2023 "TOMOSAXS: MULTIMODAL VOLUMETRIC ANALYSIS OF COLLAGEN NANO-TO-MICROSTRUCTURE ", UK |
| Year(s) Of Engagement Activity | 2023 |
| Description | E Newham talk at Biomedeng24 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | E Newham talk at Biomedeng24, "TOMOSAXS ANALYSIS OF INTERVERTEBRAL DISC BIOMECHANICS USING SYNCHROTRON X-RADIATION ", UK |
| Year(s) Of Engagement Activity | 2024 |
| Description | H Gupta, BioMedEng22 Programme Committee. |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | H Gupta was invited to join the BioMedEng22 Programme Committee. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Invited panelist, PD Lee, 2021 HCA General Meeting |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | PD Lee was invited as a panelist at "Orthogonal and Complementary Approaches" panel at the Human Cell Atlas General Meeting 2021. |
| Year(s) Of Engagement Activity | 2021 |
| Description | J Chen talk at BioMedEng24 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | J Chen talk at BioMedEng24, "Synchrotron tomography-based finite element models reveal association between osteoporosis and intervertebral degeneration", London, UK |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://biomedeng.org/biomedeng24/ |
| Description | J Chen talk at ESB 2024 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | J Chen talk at ESB 2024 "SYNCHROTRON TOMOGRAPHY-BASED FINITE ELEMENT ANALYSIS OF RAT VERTEBRAL ENDPLATES", UK |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://esbiomech2024.org/ |
| Description | MSMaH team volunteering at Harwell Open Week |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Over 30 members of MSMaH team volunteered at the Harwell Open Week on 28 and 29 June 2024, including running a stand of using 3D pen to repair damaged turbine blades, demonstraion of 3D printing equipment, using a machine build with Lego to show concept of X-ray tomography, and presenting 3D printed organs. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.harwellcampus.com/discover/stories/open-day-2024/ |
| Description | MSMaH team volunteering at UCL Festival of Engineering |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Over 30 members of MSMaH team volunteered at the UCL Festival of Engineering on 18-20 July 2024, including running a stand of using 3D pen to repair damaged turbine blades and presenting 3D printed human organ atlas. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.eventbrite.com/cc/ucl-festival-of-engineering-friday-3185929 |
| Description | PD Lee presented at CIFAR meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | PD Lee presented at CIFAR meeting, Catalyst projects update, USA |
| Year(s) Of Engagement Activity | 2024 |
| Description | PD Lee talk at CZI Conference |
| 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 talk at CZI Conference, "Deep Tissue Imaging", Online |
| Year(s) Of Engagement Activity | 2024 |
| Description | PD Lee talk at Hard X-ray Imaging of Biological Soft Tissues |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | PD Lee talk at Hard X-ray Imaging of Biological Soft Tissues, "Imaging Intact Human Organs with Near-cellular Resolution using Hierarchical Phase-Contrast Tomography", The Francis Crick Institute, UK |
| Year(s) Of Engagement Activity | 2023 |
| Description | PD Lee talk at TomoSAXS Workshop |
| 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 talk at TomoSAXS Workshop "SAXS imaging and tomography science and experimental methods", Harwell |
| Year(s) Of Engagement Activity | 2022 |
| Description | PD Lee, Invited Talk at 24 Hour Human Reference Atlas Event |
| 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, Invited Talk at 24 Hour Human Reference Atlas Event, "Mapping Whole Human Organs at High Resolution" |
| Year(s) Of Engagement Activity | 2022 |
| Description | Participation in an open day or visit at my research institution - Open Days/Public Visits |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | At Diamond's open days, visitors are able to engage with scientists and engineers as part of a visit to the facility. They encounter researchers discussing their work, and are able to see the potential future impact of the research activity, for example, the potential applications of solar technology. The beamline takes part in open days for the public and for schools. Events provoke discussion with visitors, and raise awareness of current research For the beamline. Families often bring children to the facility, who are exposed to a range of science and engineering careers outside of the usual lab environment. |
| Year(s) Of Engagement Activity | 2022 |
| URL | http://www.diamond.ac.uk/Home/Events/Inside-Diamond---Public-Open-Days.html |
| Description | Poster, A Parmenter, ICTMS 2022 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Poster, A Parmenter, ICTMS 2022, Imaging and Quantification of the Vertebral Disc-Endplate System |
| Year(s) Of Engagement Activity | 2022 |
| Description | Talk by Elis Newham at European Society of Biomechanics Congress 2023 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk by Dr. Elis Newham at the European Society of Biomechanics Congress 2023 "TomoSAXS: multimodal Mechanics from the molecular to the macro-scale" |
| Year(s) Of Engagement Activity | 2023 |
| Description | Talk, C Disney, ICTMS 2022 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Talk, C Disney, ICTMS 2022, REGIONAL VARIATION OF FIBRE KINEMATICS IN THE INTERVERTEBRAL DISC |
| Year(s) Of Engagement Activity | 2022 |
| Description | Talk, C Disney, ToScANA 2021 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | C. Disney, B.K. Bay, C.P. Winlove, J. Chen. "Micro- structure and mechanics of intervertebral disc degeneration using synchrotron tomography", ToScANA 2021 |
| Year(s) Of Engagement Activity | 2021 |