Health and Bioscience IDEAS - Imaging, Data structures, gEnetics and Analytical Strategies
Lead Research Organisation:
University College London
Department Name: Institute of Neurology
Abstract
We will develop a training program for researchers at universities, hospitals, and businesses that helps them better use data from medical images in their research. These images are generated from many different machines, such as microscopes, magnetic resonance imaging (MRI) scanners, and computer tomography (CT) scanners. These technologies not only can produce maps of the human body's structure (from single cells to large organs), but they can also tell you how the body is functioning, such as how blood is being delivered to different parts of the body or where abnormal proteins that could cause Alzheimer's disease are present. These images have played a major part in many recent scientific discoveries across a range of medical fields. As a result, imaging data is being used more often in research and the amount of imaging data available for researchers to work with and ask new scientific questions is also growing rapidly. This means that researchers from a diverse set of backgrounds now have the opportunity to work with imaging data and bring their own expertise and perspective to answering new questions about various diseases. However, this imaging data is often complex and difficult to work with, specialist training is required to understand how to handle, process, and obtain accurate and reliable information from these images. This training is often not a part of most scientists' standard curriculum, so it can be an entry barrier for many scientists in terms of getting started with research involving imaging.
We are proposing a series of short courses that will cover many different aspects of working with medical imaging data. Most importantly, as security of the sensitive personal data contained in imaging becomes a greater concern, we will focus on teaching attendees about best practices in terms of data management and protection. Some of these courses will be given as intensive face-to-face workshops, while others will be online courses where the users will set their own pace. The courses will cover a wide range of backgrounds, from newcomers who are just getting started working with imaging data to those who wish to do more advanced, complex analysis. We will also develop some courses that will allow a smaller set of individuals be able to train staff at their own institutions about how to work with this imaging data. We have experts in all of these aspects who will develop the lectures and exercise for the courses, and we will hire a course leader who will combine this content into a cohesive set of courses about medical imaging. Feedback will be sought from those attending the courses, as to assess their effectiveness, tailor them to the needs of the community, and improve them. By the end of the two years, we will make this project self-sufficient after the 2 years; the resulting courses will continue to be delivered to new researchers, with a charge that is both fair and good value to attendees throughout the UK, while also being sustainable financially from the university's perspective. During the project we will create and nurture a network that starts with fostering interaction between attendees during and after the course, creating a community of these "imaging literate" researchers throughout the UK. We hope this will lead to a range of collaborations and critical-mass for exiting and large projects.
We are proposing a series of short courses that will cover many different aspects of working with medical imaging data. Most importantly, as security of the sensitive personal data contained in imaging becomes a greater concern, we will focus on teaching attendees about best practices in terms of data management and protection. Some of these courses will be given as intensive face-to-face workshops, while others will be online courses where the users will set their own pace. The courses will cover a wide range of backgrounds, from newcomers who are just getting started working with imaging data to those who wish to do more advanced, complex analysis. We will also develop some courses that will allow a smaller set of individuals be able to train staff at their own institutions about how to work with this imaging data. We have experts in all of these aspects who will develop the lectures and exercise for the courses, and we will hire a course leader who will combine this content into a cohesive set of courses about medical imaging. Feedback will be sought from those attending the courses, as to assess their effectiveness, tailor them to the needs of the community, and improve them. By the end of the two years, we will make this project self-sufficient after the 2 years; the resulting courses will continue to be delivered to new researchers, with a charge that is both fair and good value to attendees throughout the UK, while also being sustainable financially from the university's perspective. During the project we will create and nurture a network that starts with fostering interaction between attendees during and after the course, creating a community of these "imaging literate" researchers throughout the UK. We hope this will lead to a range of collaborations and critical-mass for exiting and large projects.
Technical Summary
Imaging and genetic analysis have dramatically transformed medicine and bioscience in a short period of time. This transformation has been so fast that a substantial knowledge gap has developed between most scientists/clinicians and the computational experts. While open-source methods for data structuring and analysis can provide an equilibrating force, the expertise to apply these responsibly and effectively is lacking. Researchers must also balance open science mandates with data protection law, creating complex challenges surrounding collecting, managing, analysing and sharing imaging data, particularly when integrating with genetic data. Our consortium will produce a series of face-to-face and virtual workshops, as well as self-directed online courses and tools to close the knowledge gap for clinical and imaging science researchers in the UK and beyond. This content will cover handling imaging and genetic data, data protection, data sharing, and code sharing; with hands-on activities (such as hackathons) to help attendees develop skills while addressing their research. We will generate a core curriculum that will subsequently be tailored to fit the skill levels and research domain of the attendees. We will target this training at researchers who are based at universities, hospitals, and the burgeoning UK biotech industry. A large majority of these researchers will be clinicians, basic scientists, epidemiologists, and medical physicists, among others. At the completion of this grant, we will have established a course that will produce good results for the researchers and thus good feedback and reputation, and we will continue to offer this content at a price that represents good value for potential attendees while maintaining financial stability and support from the university.
Organisations
- University College London (Lead Research Organisation)
- University College London (Collaboration)
- University of Wisconsin-Madison (Collaboration)
- VU University Medical Center (Collaboration)
- University of Gothenburg (Collaboration)
- Washington University in St. Louis (Collaboration)
- UK Dementia Research Institute (Collaboration)
- UNIVERSITY OF OXFORD (Collaboration)
- Lund University (Collaboration)
- Institute of Cancer Research UK (Collaboration)
- Fondation Plan Alzheimer (Collaboration)
- Centre for Addiction and Mental Health (CAMH) (Collaboration)
- Alzheimer's Association (Collaboration)
Description | Health and Bioscience IDEAS - Imaging, Data structures, gEnetics and Analytical Strategies |
Amount | £799,402 (GBP) |
Funding ID | MR/V03863X/1 |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 03/2021 |
End | 12/2023 |
Title | Improvements to software packages to allow online demos on the cloud. |
Description | We modified two repositories of widely used disease progression modelling packages in Python to allow users from around the world to learn about these techniques interactively without needing to install them on their computers. This allows users who are just getting started with these techniques to learn the concepts without the distraction of the technical setup of their own development environment. We applied these to two techniques: the Event Based Model (https://github.com/HealthBioscienceIDEAS/kde_ebm) and Subtpye And Stage Inference (SuStaIN - https://github.com/HealthBioscienceIDEAS/pySuStaIn). |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | These online demos use Binder (http://mybinder.org) to launch a virtual computer on the cloud with all necessary software installed and web access to the online notebook that explains how to run the code so that all users need to learn these methods is a decent internet connection. The latter adaptation was used as part of a workshop ran by the creators of SuStaIn to demonstrate how to use the package with the video from the event online found at https://youtu.be/xzs4TL9_kZw |
URL | https://github.com/HealthBioscienceIDEAS/pySuStaIn |
Title | Interactive demo of data harmonisation |
Description | For a workshop hosted by the DEMON network, we created an interactive hands-on demo that attendees could use themselves without the need to install any software on their machine. This was done using Binder (https://mybinder.org), which creates a virtual machine on the cloud based on a github repository, such that all the required software installed on the virtual machine and users can access a teaching notebook in Python or R that goes through the concepts. |
Type Of Material | Computer model/algorithm |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | Users and attendees have the ability to understand how to use these data harmonisation strategies before grappling with various challenges that might come from installing it on their own machines. |
URL | https://github.com/HealthBioscienceIDEAS/demon-imaging-harmonisation |
Title | Online demonstration of reproducible medical imaging pipelines |
Description | As part of the UCL Medical Imaging Computing Summer School, we created a demo to illustrate the power of modern imaging data management platforms with reproducible medical imaging pipelines. We created a project that involved individuals storing imaging data into a web-based image data management platform called XNAT. We created artificial identifying information for each of the medical image sets and helped people understand the importance of de-identifying the underlying metadata in the image's data structure. We then created Docker images that ensured reproducible imaging analysis and showed individuals how to run them all through the XNAT, providing a much simpler interface for users to process data than the command line that is commonly required. Finally, we asked individuals to do an extra de-identification step, mainly reducing the facial features of an individual, and asked them to investigate whether the results from the same imaging analysis were changed. The documentation for this project is available as our the containers, but we were not able to release the entire repository because at the time it relied on UCL specific infrastructure. We are in the process of refining the repository so that in the future, individuals will be able to try it on their own infrastructure |
Type Of Material | Data handling & control |
Year Produced | 2021 |
Provided To Others? | No |
Impact | Feedback we got from the attendees indicated that they had a better understanding of why imaging data management systems would be important for their research and a better understanding of the compute resources that are required for some analyses. |
URL | https://healthbioscienceideas.github.io/MedICSS-Project-Repro-Pipelines/ |
Description | Carpentries' sMRI lesson material collaboration |
Organisation | Centre for Addiction and Mental Health (CAMH) |
Country | Canada |
Sector | Hospitals |
PI Contribution | Up to now, this has been only a point of contact and making plans how our efforts could be combined to deliver more courses around neuroimaging. They have already two courses at a usable level, though still in beta: - Introduction to dMRI (https://carpentries-incubator.github.io/SDC-BIDS-dMRI/), and - Structural MRI (Pre)processing and Neuroimaging Analysis (https://carpentries-incubator.github.io/SDC-BIDS-sMRI/) |
Collaborator Contribution | Provided ideas about making the notes more sustainable and easier to maintain. |
Impact | Obtained first-hand experiences of a similar training material following the Carpentries style. |
Start Year | 2021 |
Description | Collaboration with DRI about new microscopy short course |
Organisation | UK Dementia Research Institute |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | We have developed a new course on working with microscopy imaging data. This course is currently a two day-interactive workshop that covers basic data structures of imaging, designing microscopy experiments and basic image analysis pipelines. We have engaged with experts in the field to identify what these training areas as being the most needed for new researchers in the field. |
Collaborator Contribution | We have enlisted experts on microscopy data from the UK Dementia Research Institute at UCL (Nicolas Cade, Giampietro Schiavo, Tammaryn Lashley) to create the structure for the course. The partners have also provided feedback into the design and delivery of the workshop, providing some attendees for the first run of the workshop that will take place in April. |
Impact | Content for the workshop course |
Start Year | 2023 |
Description | Collaboration with EU-MIND and Fondation Alzheimer to deliver training |
Organisation | Fondation Plan Alzheimer |
Country | France |
Sector | Charity/Non Profit |
PI Contribution | Based on our successful training workshops as part of the Alzheimer's Association International Conference, we have made an agreement with the French Alzheimer's disease foundation Fondation Alzheimer to deliver this workshop at a new conference (EU-MIND) they are organising for European researchers who work with neuroimaging in dementia. |
Collaborator Contribution | The partners have helped us with the organization of the workshop and have proposed financial support for travel/hotel for the organizers of the training session and related costs of the workshop (budgeted to be about 4600 euros as mentioned above). |
Impact | None yet - workshop scheduled for September 2024 |
Start Year | 2023 |
Description | Collaboration with Learn To Discover UKRI DaSH programme |
Organisation | University College London |
Department | Department of Cell and Developmental Biology |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have planned a group of workshops together involving Working with the command line and Python coding with a focus on medical imaging. |
Collaborator Contribution | We worked equally in developing and delivering lectures as part of this workshop. |
Impact | A series of coding workshops for researchers. |
Start Year | 2022 |
Description | Collaboration with Medical Phyiscs department to deliver short courses |
Organisation | University College London |
Department | Department of Medical Physics and Biomedical Engineering |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | With one of the key members of IDEAS now a lecturer at Medical Physics and many of our short courses aligned with their curricula, we have decided to work with this department to produce short courses, the first of which being medical image registration and machine learning in medical imaging. Partners that are based at Medical Physics but part of IDEAS are developing the content. |
Collaborator Contribution | The administrative team at Medical Physics will help organize, advertise and do outreach to potential attendees for these courses. They will be advertised on UCL's short courses web pages. |
Impact | * No outputs yet |
Start Year | 2023 |
Description | Partnering with Alzheimer's Association to deliver pre-conference workshops. |
Organisation | Alzheimer's Association |
Country | United States |
Sector | Charity/Non Profit |
PI Contribution | We developed the overall content and plan for the workshop, some of the lessons and the computational infrastructure used to deliver the lessons. |
Collaborator Contribution | The Alzheimer's Association provided us the opportunity to delivery training workshops on neuroimaging as part of the pre-conference to their large Alzheimer's Association International Conference. They organized the venue and ran the registration. Luigi Lorenzini (VUMC), Tobey Betthauser (University of Wisconsin), Alexa Pichette-Binault (Lund), Ludovica Griffanti (Oxford), and Alexis Moscoso (Gothenburg) were expert lecturers who developed and taught elements of the workshop. |
Impact | * 2022 Getting Started With Neuroimaging Workshop * 2023 Getting Started With Neuroimaging Workshop * The Basics of Neuroimaging Webinar Series. |
Start Year | 2021 |
Description | Partnering with Alzheimer's Association to deliver pre-conference workshops. |
Organisation | Lund University |
Country | Sweden |
Sector | Academic/University |
PI Contribution | We developed the overall content and plan for the workshop, some of the lessons and the computational infrastructure used to deliver the lessons. |
Collaborator Contribution | The Alzheimer's Association provided us the opportunity to delivery training workshops on neuroimaging as part of the pre-conference to their large Alzheimer's Association International Conference. They organized the venue and ran the registration. Luigi Lorenzini (VUMC), Tobey Betthauser (University of Wisconsin), Alexa Pichette-Binault (Lund), Ludovica Griffanti (Oxford), and Alexis Moscoso (Gothenburg) were expert lecturers who developed and taught elements of the workshop. |
Impact | * 2022 Getting Started With Neuroimaging Workshop * 2023 Getting Started With Neuroimaging Workshop * The Basics of Neuroimaging Webinar Series. |
Start Year | 2021 |
Description | Partnering with Alzheimer's Association to deliver pre-conference workshops. |
Organisation | University of Gothenburg |
Country | Sweden |
Sector | Academic/University |
PI Contribution | We developed the overall content and plan for the workshop, some of the lessons and the computational infrastructure used to deliver the lessons. |
Collaborator Contribution | The Alzheimer's Association provided us the opportunity to delivery training workshops on neuroimaging as part of the pre-conference to their large Alzheimer's Association International Conference. They organized the venue and ran the registration. Luigi Lorenzini (VUMC), Tobey Betthauser (University of Wisconsin), Alexa Pichette-Binault (Lund), Ludovica Griffanti (Oxford), and Alexis Moscoso (Gothenburg) were expert lecturers who developed and taught elements of the workshop. |
Impact | * 2022 Getting Started With Neuroimaging Workshop * 2023 Getting Started With Neuroimaging Workshop * The Basics of Neuroimaging Webinar Series. |
Start Year | 2021 |
Description | Partnering with Alzheimer's Association to deliver pre-conference workshops. |
Organisation | University of Oxford |
Department | Oxford Centre for Functional MRI of the Brain (FMRIB) |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We developed the overall content and plan for the workshop, some of the lessons and the computational infrastructure used to deliver the lessons. |
Collaborator Contribution | The Alzheimer's Association provided us the opportunity to delivery training workshops on neuroimaging as part of the pre-conference to their large Alzheimer's Association International Conference. They organized the venue and ran the registration. Luigi Lorenzini (VUMC), Tobey Betthauser (University of Wisconsin), Alexa Pichette-Binault (Lund), Ludovica Griffanti (Oxford), and Alexis Moscoso (Gothenburg) were expert lecturers who developed and taught elements of the workshop. |
Impact | * 2022 Getting Started With Neuroimaging Workshop * 2023 Getting Started With Neuroimaging Workshop * The Basics of Neuroimaging Webinar Series. |
Start Year | 2021 |
Description | Partnering with Alzheimer's Association to deliver pre-conference workshops. |
Organisation | University of Wisconsin-Madison |
Department | School of Medicine and Public Health |
Country | United States |
Sector | Academic/University |
PI Contribution | We developed the overall content and plan for the workshop, some of the lessons and the computational infrastructure used to deliver the lessons. |
Collaborator Contribution | The Alzheimer's Association provided us the opportunity to delivery training workshops on neuroimaging as part of the pre-conference to their large Alzheimer's Association International Conference. They organized the venue and ran the registration. Luigi Lorenzini (VUMC), Tobey Betthauser (University of Wisconsin), Alexa Pichette-Binault (Lund), Ludovica Griffanti (Oxford), and Alexis Moscoso (Gothenburg) were expert lecturers who developed and taught elements of the workshop. |
Impact | * 2022 Getting Started With Neuroimaging Workshop * 2023 Getting Started With Neuroimaging Workshop * The Basics of Neuroimaging Webinar Series. |
Start Year | 2021 |
Description | Partnering with Alzheimer's Association to deliver pre-conference workshops. |
Organisation | VU University Medical Center |
Country | Netherlands |
Sector | Academic/University |
PI Contribution | We developed the overall content and plan for the workshop, some of the lessons and the computational infrastructure used to deliver the lessons. |
Collaborator Contribution | The Alzheimer's Association provided us the opportunity to delivery training workshops on neuroimaging as part of the pre-conference to their large Alzheimer's Association International Conference. They organized the venue and ran the registration. Luigi Lorenzini (VUMC), Tobey Betthauser (University of Wisconsin), Alexa Pichette-Binault (Lund), Ludovica Griffanti (Oxford), and Alexis Moscoso (Gothenburg) were expert lecturers who developed and taught elements of the workshop. |
Impact | * 2022 Getting Started With Neuroimaging Workshop * 2023 Getting Started With Neuroimaging Workshop * The Basics of Neuroimaging Webinar Series. |
Start Year | 2021 |
Description | Partnership around XNAT workshop organisation. |
Organisation | Institute of Cancer Research UK |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Three of our team members were part of the organising committee for an international workshop for users and developers of an image data management platform called XNAT. We met weekly for a six month buildup before the workshop took place to prepare the workshop agenda. Our group identified and approached speakers to participate in the workshop, and we were responsible for the online platform that was used to host a majority of the workshop's content. We assisted on the administration of the event on the day, as well as charging a session and providing a poster for the virtual poster session. We continued this relationship and developed an in-person workshop for September 2022. |
Collaborator Contribution | The main partners were also part of the steering committee. Washington University provided experts to speak at the workshop, organised sessions and handled registration. ICR and NCITA also contributed expertise and talks for the workshop, setting up the virtual poster session and developed some of the promotional and communications material for the meeting. All of the partners contributed in a similar fashion in terms of organising the workshop in 2022. The Wash U and Flywheel groups developed lectures and demonstrations built in the cloud for attendees to use. THey also hosted one dinner for attendees. The UCL group organized the venue, some of the lectures, served on panels, and hosted one welcome reception. |
Impact | Hosting the 2021 XNAT International workshop virtually and the 2022 in-person workshop in London. |
Start Year | 2021 |
Description | Partnership around XNAT workshop organisation. |
Organisation | Washington University in St Louis |
Department | School of Medicine |
Country | United States |
Sector | Academic/University |
PI Contribution | Three of our team members were part of the organising committee for an international workshop for users and developers of an image data management platform called XNAT. We met weekly for a six month buildup before the workshop took place to prepare the workshop agenda. Our group identified and approached speakers to participate in the workshop, and we were responsible for the online platform that was used to host a majority of the workshop's content. We assisted on the administration of the event on the day, as well as charging a session and providing a poster for the virtual poster session. We continued this relationship and developed an in-person workshop for September 2022. |
Collaborator Contribution | The main partners were also part of the steering committee. Washington University provided experts to speak at the workshop, organised sessions and handled registration. ICR and NCITA also contributed expertise and talks for the workshop, setting up the virtual poster session and developed some of the promotional and communications material for the meeting. All of the partners contributed in a similar fashion in terms of organising the workshop in 2022. The Wash U and Flywheel groups developed lectures and demonstrations built in the cloud for attendees to use. THey also hosted one dinner for attendees. The UCL group organized the venue, some of the lectures, served on panels, and hosted one welcome reception. |
Impact | Hosting the 2021 XNAT International workshop virtually and the 2022 in-person workshop in London. |
Start Year | 2021 |
Description | "The Basics of Neuroimaging" webinar series |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | I was invited by the Alzheimer's Association to organize a 5-part webinar series "The Basics of Neuroimaging", along with the other instructors of our IDEAS-funded training course "Getting Started With Neuroimaging Analysis". I was the expert speaker for the "Basics of MRI" session and provided a 25 minute overview of how sturctural MRI is key in dementia research, as well as potential for use in care. I also was the moderator for other sessions in this series. As with all Alzheimer's Assocation webinars, these are available for viewing on-demand. |
Year(s) Of Engagement Activity | 2023 |
URL | https://training.alz.org/Research-Webinars |
Description | Conference workshop "Getting Started with Neuroimaging Analysis" |
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 | In coordination with the Alzheimer's Association, and members of world-class research institutions from around the world, we developed an introductory hands on session for working with neuroimaging data that was held as a satellite pre-conference workshop to the Alzheimer's Association International Conference in San Diego in July 2022. In order to make this project very inclusive and to avoid potential issues with different laptops, we created a virtual machine on the cloud with all of the needed specialist neuroimaging analysis software pre-loaded so that users did not have any trouble setting up and installing the requirements. The course covered working with command line applications often found in neuroimaging applications, the basics of data structures used in imaging, and structural, functional, and diffusion-based magnetic resonance imaging (MRI) data. We conducted this workshop again at AAIC 2023 with an increased attendence of 40, taking on feedback from the original session to further improve it. The 2023 received a rating of 9.4 out of 10 (14 responses received from 40 attendees) in terms of how likely they would be to recommend the workshop to a colleague. Nearly all the attendees either agreed or strongly agreed with the statements "I felt comfortable learning in this workshop", "I can immediately apply what I learned at this workshop", and "I achieved what I expected to get out of this workshop". Some additional feedback includes: "Pre workshop webinars and multiple instructors and individually tailored help" "Simple and straight forward. Helpful facilitators." "Everything was great! Easy to get very good answers to questions." "Well prepared instructions and data. Skilled monitors." "The use of VM's, and the preparation's with the data beforehand. As well has having the webinars before the actual workshop" "It was fun and very useful!" |
Year(s) Of Engagement Activity | 2022,2023,2024 |
URL | https://healthbioscienceideas.github.io/aic2023-workshop/ |
Description | Delivered invited lecture and weeklong project for UCL Medical Image Computing Summer School |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | MedICSS (UCL Medical Image Computing Summer School) is an annual summer school organised and run by the Centre for Medical Image Computing (CMIC) and Wellcome-EPSRC Centre for Interventional and Surgical Sciences (WEISS).. It is intended for any individuals regardless of their careers stage who are interested in medical image computing for their research.. Multiple members of the IDEAS team contributed lectures to the program that cover essential elements of imaging that we wish to highlight as part of this project: 1. David Cash gave a talk entitled "Medical Imaging at scale". It covered strategies for handling, storing, and processing larger medical imaging datasets. It also helped attendees understand where open science and data protection have shared goals and where there are potential conflicts. 2, Jamie McClelland gave a talk entitled "Medical Image Registtration: A Brief Introduction" - which provided the overview of image registration, the fundamental elements that make up a medical image registration framework and how these elements differ depending on the application, and validating the results of the registration after it has been performed. 3. Andre Altmann gave a talk entitled "Combining genetics and imaging to better understand brain disorders" which looks at ways of combining imaging biomarkers with genetic analyses to better understand what are the genetic factors driving the prevalence of image-derived phenotypes. In addition to the lectures, there were also week-long projects that were developed, where students worked in teams in an assigned task for two hours each for the first four days, followed by a presentation of their findings on the final day. Andre Altmann lead a project on Imaging Genetics, which gave project members a hands-on introduction to imaging genetics analyses, both using more classic case-cotrol approaches as well as multivariate methods. David Cash and Haroon Chughtai, a member of the Research Software Development Group who works closely with IDEAS, created a project that covered the principles of data management and using reproducibility friendly technology, such as Docker or Singularity containers, to run the analysis. We also examined how the reproducibility of results is affected by removing the facial features (known as "de-facing") from a brain MRI image, a data protection strategy often implemented by researchers. This is because these facial features can potentially identify an individual, currently only in very controlled circumstances, However, these defacing algorithms are not completely benign; they can have unintended consequences to the popular neuroimaging pipelines that are often used to analyse the data. So the project attendees ran image analysis before and after de-facing to see how much de-facing affected the results, thus getting an appreciation for the balance between data protection and reproducibility. IDEAS was heavily involved in the 2022 editon UCL Medical Imaging Computing Summer School, with two of its members, Kris Thielemans and Maria Tziraki, being on the three-member organising committee, as well as contributing lectures and projects for the attendees. There is plan for the lecture and workshop to continue this year. |
Year(s) Of Engagement Activity | 2021,2022 |
URL | https://medicss.cs.ucl.ac.uk/ |
Description | Email list for announcing courses |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | We have created a JISC-hosted email list at HEALTHBIOSCIENCE-IDEAS-NEWS@JISCMAIL.AC.UK to handle announcements for upcoming courses of interest to our subscribers. There are links to subscription available on the website and social media channels. Curreently there are 23 subscribers and we will ramp up engagement onthis as more courses come online. |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.jiscmail.ac.uk/HEALTHBIOSCIENCE-IDEAS-NEWS |
Description | Health and Bioscience IDEAS website |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | We have created a website for the project, which is where courses will be announced and information about the project can be found. This has been established using the GitHub pages functionality within GitHub, This provides free hosting of the website, and it allows the content to be edited through simple interaction with plain text Markdown files. We also use it to demonstrate some of the practices around software development in research that we wish to promote, like the use of a source code versioning system, and effective continuous integration testing to ensure that the website will always be functional after edits are deployed. |
Year(s) Of Engagement Activity | 2021 |
URL | https://healthbioscienceideas.github.io/ |
Description | Invited lecture for early career researchers in artificial intelligence for Alzheimer's disease. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | We were invited by early career researchers from the DEMON network (https://demondementia.com/) to give a talk/tutorial as part of their online workshop entitled "ECR DEMON workshop: combining imaging data using machine learning". We provided an interactive hands-on lecture on data harmonisation - the need for harmonising across different MRI scanners, and strategies for achieving harmonisation. |
Year(s) Of Engagement Activity | 2021 |
URL | https://healthbioscienceideas.github.io/demon-imaging-harmonisation/ |
Description | Software Caprentries workshop on Python and Imaging Analysis. |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Professional Practitioners |
Results and Impact | UCL typically provides Software Carpentries style courses that cover an introduction to the command line, working with git version control, and basic programming with Python. One comment we heard from previous attendees was that after these events it was not clear how to actually implement what they learned into medical imaging research. As a result, we built a new version of the course that covered the original two days of material mentioned above, but also covered how to use Python for various image processing exercises, using both MRI and microscopic data examples. All the code was taught interactively using Jupyter notebooks and in reproducible Python environments so that everyone could run the code on their own laptops. This course has now been run successfully twice: once in September 2022 and again in March 2023. Each event has a capacity of 30 individuals and all events have been sold out so far. |
Year(s) Of Engagement Activity | 2022,2023 |
URL | https://github-pages.ucl.ac.uk/2023-03-09-UCL-DasH/ |
Description | SyneRBI-XNAT hackathon 2023 |
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 | Our teams joined the XNAT workshop 2022 https://wiki.xnat.org/workshop-2022/ hackathon with a topic on uploading MR raw data into the XNAT database. Participants benefited from learning about the XNAT software as well as MR raw data formats and requirements. This will lead to increased capabilities of the XNAT database and wider use of MR raw data by researchers, enabling integrated reconstruction pipelines in the future. It is also a first step towards integrating PET raw data into XNAT. |
Year(s) Of Engagement Activity | 2022 |
URL | https://wiki.xnat.org/workshop-2022/xnat-workshop-2022-hackathon-projects#XNATWorkshop2022HackathonP... |
Description | Team Coders workshop on EBM |
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 | In partnership with the UCL Academic Career Office, we developed a "hackathon" style collaborative learning activity around Python and data driven disease progression models. The project grouped researchers into teams and walked them through the process of extracting imaging biomarkers used in Alzheimer's disease, data wrangling and visualisation, and finally how to implement a widely used disease progression model called the Event Based Model that has been used on publicly available data to help better determine the ordering of various disease processes. The goal for each team was to build up the data set and then replicate the analysis of a well-known journal article. The initial test event took place in the fall of 2022, with a capacity of 16. The workshop was sold out with a long waiting list. User feedback was positive and constructive, with some attendees offering to serve as facilitators on the next iteration, which took place in June of 2023. |
Year(s) Of Engagement Activity | 2022,2023 |
URL | https://healthbioscienceideas.github.io/TeamCoders_Event_Based_Model/ |
Description | Twitter handle for the project. |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | We have set up a project twitter handle to promote awareness of the project as well as the courses that we will run as well as relevant efforts hosted by other groups. |
Year(s) Of Engagement Activity | 2021 |
URL | https://twitter.com/HealthBioIdeas |
Description | XNAT Workshop 2022 London |
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 | After the success of the virtual workshop in 2021, we hosted an in-person workshop in London from 31 October - 4 November 2022. This was a five-day event with over 90 individuals attending, one-third of which were UK-based researchers, and the rest from 9 other countries (Australia, USA, Belgium, Switzerland, Germany, Holland, Italy, Luxembourg and Spain). This was primarily an educational event, with tutorial sessions on how to setup and use various core and new features of XNAT. It also included hackathon activities, where people could get involved with developing new features alongside experts. |
Year(s) Of Engagement Activity | 2022 |
URL | https://wiki.xnat.org/workshop-2022/ |
Description | XNAT workshop 2021 |
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 | The workshop was attended by over 200 participants from 19 countries (United Kingdom, United States, Australia, Colombia, Germany, Netherlands, Japan, Canada, France, Italy, Spain, China, Greece, Switzerland, Portugal, Belgium, Ukraine, Singapore, India). Attendees came from many disciplines: developers of the platform, researchers who use it to manage and analyse their data, principal investigators who rely on it for their clinical research studies, and development operations specialists whos job it is to install and maintain instances at their institutions. The format was extremely interactive. While there were a few keynote speakers, there were also round table discussions with expert speakers and town hall forums where attendees were allowed to have their say on the current state of the platform and its direction in the future. Use of the online Q&A and chat functions were heavy. provided for lots of discussions during the sessions. There was also a virtual poster hall and poster session using the online spatial conferencing platform Spatial Chat. The videos of the talks from the session as well as the posters from online poster session are still available to view from the above URL. Many of these recorded elements are there to provide training and advice to potential, new and active users of the system, of which the United Kingdom represents the second largest group of users, just behind the United States. |
Year(s) Of Engagement Activity | 2021 |
URL | https://wiki.xnat.org/workshop-2021/ |