Research Computing and Imaging

Lead Research Organisation: University of Leeds
Department Name: Sch of Computing

Abstract

Today, images are everywhere and are increasingly used in science. There are many examples of the importance of images over the history of science, a classic example being the motion sequence photographs of Eadweard Muybridge taken in 1878. These showed for the first time that for a brief moment when a horse gallops none of its feet are on the ground, thus capturing the truth through photography and paving the way for the development of the motion-picture industry ten years later.

Imaging science is the multidisciplinary pursuit concerned with generating, collecting, analysing, enhancing, and visualizing images. Despite the UK being strong in imaging and having many strategic centres of excellence supporting a variety of imaging methods it currently lacks integration with research computing, which is essential for processing and understanding the detail of these images. These facilities are traditionally based around one imaging method but this fellowship copies the SCI (Scientific Computing and Imaging) Institute in Utah which is an international centre of excellence where software is developed across the range of imaging methods and for the variety of disciplines that use images. This approach allows knowledge to be transferred and software re-purposed across a variety of imaging communities. In the long term, by major goal is to develop a centre of excellence at UoL similar to the SCI Institute.

There are two strands to the fellowship; the first is to develop software while the second is to upgrade computational skills and develop a computational community for imaging.

In this fellowship I will work with two of these national imaging facilities to develop software for a number of strategic case studies. Seven of these will based around new spectral imaging methods along with an initial training case in super-resolution light imaging. The new spectral imaging methods are novel because they include spectroscopy information for each pixel or voxel of the 2D or 3D image. The fundamental physical principles for extracting the exact structural chemical information in spectroscopic X-ray and electron micrograph (em) images are now well established, but there are no software packages that implement the whole of this computational workflow. This fellowship will develop easy-to-use software for 2D, 3D and 4D visualization of X-ray and em images, integrating software tools, re-purposing algorithms and designing new visualization techniques.

This fellowship will also upgrade computing skills in imaging at UoL. I will do this by working with a stakeholder group which includes four senior researchers. The PDRA and I will develop software for them, and those they collaborate with, and I will mentor one of their researchers who support others in their research groups. Knowledge from this mentoring will inform me about what training materials need to be developed on campus. I will also lead three computational networks at the UoL which will be advertised across the N8 (Northern 8 Universities). There will be one meeting a month across these networks which includes an annual one day conference for each of the networks.

While working on these two objectives I will continue to develop professionally and further develop my research into the role of the RSE. With help from the SSI I will disseminate this research and campaign for the RSE role both at UoL and nationwide.

Planned Impact

Imaging is increasingly used in science because it is a leading technology platform that enables discoveries in many disciplines. The UK has a number of internationally recognised centres of excellence which are strategically important to the UK economy and society, pushing back the frontiers of our scientific knowledge. This fellowship partners with 2 of these facilities: DLS which is a large synchrotron facility and SuperSTEM which is the EPSRC National Facility for Aberration-Corrected Scanning Transmission EM, which has a range of academic and commercial partners aligned with EPSRC remit, including Computing, Mathematical Sciences, Physical Sciences, Engineering, Digital Technologies, Energy, Healthcare Technologies, and Manufacturing.

During this fellowship a series of software will be released, developed through strategic case studies that support the development of the new spectral imagining methods. While the fundamental physical principles for extracting exact structural chemical information in spectroscopic X-ray and em images are now well established, there are no existing software packages. This is typical of imaging which lacks the integration of imaging with research computing, so contributing to the lag in the adoption of new imaging methods and perpetuating a divide between experimentalists and computationalists, even though it is increasingly important to integrate the approaches.

The series of software I will release are relevant to particular industries in the UK and the design and development of new products as the case studies build on established collaborations with industry, specifically Infineum, AstraZeneca, Syngenta and Saudi-Aramco as well as with academics who also collaborate with industry. These are: 1,) the development of additives to fuels and lubricants; 2,) the formulation and manufacture of prescription pills; 3,) the design of artificial joints; 4,) improved understanding of CFD in the design of a variety of products such as nasal sprays, injections or relevant to the manufacturing of tablets, coatings or printing; 5,) the development of medical devices and tapes/seals; 6,) the development of optical coatings such as anti-reflective, self-cleaning, electrochromic, mirrors, filters and protective, aesthetic or decorative coatings; and 7,) chemical catalysis which is important to the Pharmaceutical, Agrochemical, Fine and Speciality Chemical Industries.

Software will be designed and released through DLS and SuperSTEM and integrated into their roadmaps. DLS has two relevant toolkits, (DAWN) which is designed for data as it comes straight from the beam line, and SAVU which is for the general processing of data. Software will be released into these so as to benefit from the large user communities of both academics and industrial partners that already exist. Training and tutorials will also be offered.

The stakeholder group with four senior academics in the field of imaging will benefit from software and my computational knowledge. This will feed into the Bragg Centre, the Astbury Centre and other imaging facilities on campus. I will also mentor one of their key researchers who will support other researchers. I will also contribute to the N8 centre of excellence so that any new HPC systems will be suitable for imaging.

Computational skills will be upgraded on campus through the computational networks I lead and that will be advertised across the N8. Through business development links at Leeds City Councils I will aim to find commercial speakers and network members. There will be twelve meetings each year across the three networks and these will include a one-day conference for each network.

The general public will benefit from visualizations and artists commission each year. These will be used broadly at science festivals eg, Leeds Science Festival, Astbury Conversations, Light Night Leeds, Otley Courthouse as well as at events at DLS and SuperSTEM.

Publications

10 25 50
 
Description I have worked with 3 groups of researchers to understand their research questions. From that I have identified software and computational approaches that could boost their research outputs.
Exploitation Route The computational work-flows that I am in the process of developing boost the research of a variety of stakeholders. These are in the initial phase of being developed but potentially affect a broad range of sectors.
Sectors Agriculture, Food and Drink,Chemicals,Digital/Communication/Information Technologies (including Software),Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Description Broadening the understanding of the RSE role and impact at Diamond Light Source.
First Year Of Impact 2018
Sector Other
Impact Types Cultural

 
Description Co-organised a day workshop on Visualization for HPC-SIG at the Universtiy of Birmingham on the 22nd of May 2018 and gave the talk "Remote Visualization an Overview" 
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 Academic HPC services do not tend to have interactive sessions as jobs are scheduled and so can run at any time. This results in a relatively poor understanding and use of visualization by academic HPC service providers and the academic HPC user community. This meeting was aimed at academic HPC service providers who wished to understand more about how to improve the use of visualization on their HPC services.
Year(s) Of Engagement Activity 2018
 
Description Co-organised the RSE 2018 workshop "Implicit None" C. Jones, J. Leng, K. Pringle and T. Allard 
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 Developed and gave a workshop at the RSE18 conference.
Year(s) Of Engagement Activity 2018
 
Description Delivered the training course "Visualization Basics with ParaView" at the University of Leeds 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Delivered this training that I had previously developed at the University of Leeds twice in the year. The end of the workshop allows the students to present their problems so they can get expert help and advice.
Year(s) Of Engagement Activity 2018
 
Description Developed and delivered a new training course, "Introduction to Fiji" 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Developed training materials for a Fiji (which is a version of ImageJ that comes with a selection of plugins) and delivered them once as a pilot course. The end of the course allows students to present their problems so that they can get expert help.
Year(s) Of Engagement Activity 2018
 
Description Flash talk, "Joanna Leng: What Environment Does an RSE Need?" at the Collaborations Workshop in Cardiff on 26th March 2018. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact The environments that RSE work in are little understood but can affect the quality and efficiency of their work. I used this flash presentation to run a survey of those present to try better to understand the state of practice in the UK.
Year(s) Of Engagement Activity 2018
 
Description Gave a talk, "The HPC services at the University of Leeds" at the University of Nottingham HPC User Conference on the 17th of April 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact The Nottingham HPC User Conference coincided with the start of a new HPC service there. The talk covered service delivery, skills development and RSE roles.
Year(s) Of Engagement Activity 2018
 
Description Organised a meeting and discussion on "The Benefits of having an RSE team" with the speakers Alun Ashton and Mike Croucher 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact This was the first of a series of meetings to help develop awareness of the RSE role and to build the RSE community at the University of Leeds. There were 38 people who registered and positive feedback was gained from 9.
Year(s) Of Engagement Activity 2018
 
Description Organised a talk by Gillian Arnold on "What an Amazing Place Technology is for Women" 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact This was a meetings for women in the RSE, HPC or IT community at the University of Leeds. There were 38 people who registered and positive feedback was gained from 7.
Year(s) Of Engagement Activity 2018
 
Description Organised an RSE meeting "RSE Careers and Roles: Louise Brown" for 29th January, 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact At previous events it had become clear that there is confusion over what the RSE careers and roles look like. This talk gave a practical description from an established RSE, Louise Brown who is an EPSRC funded RSE fellow.
Year(s) Of Engagement Activity 2018
 
Description Orgnised a day long workshop with hands on tutorials and discussion on, "AI and Machine Learning Workshop" on the 19th December 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact This was a day long event and networking event that was primarily aimed at developing technical skills for RSEs at the University of Leeds. RSE s tend not to have funding for personal or technical development oe travel and AI is currently important technique for an RSE to understand.The event was also open to academics and professional/support staff on campus interested in applying AI to their research or the research groups they support. The event was divided into 3 parts. In the morning there were talks that were introductory and inspiring given by David Hogg, Alicija Piotokowicz, Alistair Droop. In the afternoon there were 2 paraellel session for hands on tutorials by Jonny Hancox (NVIDIA), Jony Castagna (STFC Daresbury and NVIDIA Ambassador) and Martin Callaghan. Finally I hosted a discussion and there was a networking at the end of the day. Registration was for the each of the 3 events and 150 registered with positive feedback from 24.
Year(s) Of Engagement Activity 2018
 
Description Spoke briefly on "Research Computing and Imaging" at the EPSRC workshop for RSE fellows on the 24th of Septemeber 2108. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Supporters
Results and Impact EPSRC meeting to look at the future of the RSE fellowship scheme.
Year(s) Of Engagement Activity 2018
 
Description Spoke on "Research Computing and Imaging" at the Imaging Physics Lunchtime Seminar, University of Leeds on the 6th of February, 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact The role of the RSE is little understood or recognised. This talk was aimed at the medical imaging research community who currently need more good quality research software . This talk made them aware of this emerging role and how it differs from the standard academic role.
Year(s) Of Engagement Activity 2018
 
Description Spoke on "Research Computing and Imaging" to the Archer Champions in Manchester on the 25th of April, 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Archer is the national flagship academic HPC (high performance computer) service. The Archer Champions exists to allow information and knowledge to transfer down the tiers from national, to regional and so to local HPC services. Attendees tend to be people involved in delivering HPC services, large scale users of HPC services and representatives from the research councils that fund Archer ie EPSRC and NERC. At this meeting I disseminated information on my fellowship and RSEs.
Year(s) Of Engagement Activity 2018
 
Description Spoke on the role of the RSE and led discussions at the training course "SWD 3: Software development practices for" on the 7th February 2018 at the University of Leeds 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact The role of the RSE is little recognised and the practices of the RSE differ subtly from those of commercial software developers. This talk introduced the roles and practices of an RSE to the audience. The discussions raised topics and issues on the practices of the RSE and how those may differ to commercial practices for example research software tends to be managed at a project level rather than at a research programme level and this can affect how they use version control systems. These discussion were used by the course provider to improve their training materials.
Year(s) Of Engagement Activity 2018