To drive recognition of research software and its authors, the ARDC is running a series of monthly interviews with leading research software engineers (RSEs) to share their experience creating, sustaining and improving software for research.
This month, we spoke to Dr Robert Smith, a Senior Research Officer at The Florey Institute of Neuroscience and Mental Health and a fellow of the Australian National Imaging Facility (NIF). With a view to advance brain science, Rob focuses on developing sophisticated processing and reconstruction techniques for analysing image data, especially diffusion magnetic resonance imaging (MRI). He is one of the developers of MRtrix3, a freely available software package for neuroscience that was named a finalist for the 2024 Eureka Prize for Excellence in Research Software.
What impact has MRtrix3 had?
We know from user feedback that MRtrix3 is being used to guide clinical decision making. For instance, it’s used to determine surgical candidates and margins for brain tissue resection. We also know that one of our core analysis pipelines has been applied across a very broad spectrum of neurological disorders, for instance, as shown in this review.

One application that we’ve used a lot recently for media content was an investigation into the effects of microgravity on brain microstructure and morphology. Colourful images of brain white matter connectivity from the software are always visually impressive and presenting them in the context of space flight I think tickles everybody’s inner nerd.
I recently collaborated with researchers at the University of Melbourne to optimise a brain white matter connectivity reconstruction pipeline for brain imaging data across tens of thousands of participants in the UK Biobank. This means that a broad range of researchers using that dataset will have access to the potential biomarkers that our software aims to quantify robustly.
In another recently published project, we took one of our core analysis pipelines for discovering white matter effects in groups and tried making it operable on an individual basis. Improving the software to help classify, diagnose and detect individual brain abnormalities is the next major use of our technology. I look forward to expanding on this proof of concept and realising an even greater impact in the research and clinical community.
… MRtrix3 is being used to guide clinical decision making. For instance, it’s used to determine surgical candidates and margins for brain tissue resection … Improving the software to help classify, diagnose and detect individual brain abnormalities is the next major use of our technology.
How do you measure the usage of MRtrix3 for reporting or improvement?
We have historically hamstrung ourselves a little in this regard, partly as a consequence of keeping the barrier to access low. Unlike some of the other software in the domain, we don’t require registration for access. We entered public beta very early in development, about halfway between forking from the 0.2 version and our production release. During this time, the software was only available via building from source, and GitHub provides clone statistics for the prior 2 weeks only. So we are missing robust usage statistics for much of the software’s lifetime. Other usage numbers we pull from post-production release are GitHub tarball downloads, Anaconda installs, and DockerHub pulls.
We have a journal article describing the software API and architecture. It showcases the software engineering work we’re proud of and encourages other researchers to use it as a framework for their own development efforts. It also translates our efforts into the traditional academic currency of citations. In the 5 years since the article was published, we’ve hit 2,000 citations. We also have nearly 2,000 accounts on our community forum, which is an under-estimate of the user base considering that registration is optional.
What types of collaborations are you most interested in pursuing?
The research interactions that really engage me are where there’s a novel contribution at the intersection between scientific methodology and software implementation. Sometimes a research question needs augmented software that can only be delivered by someone who fully understands the scientific content and has the programming skills to implement it.
In a recent collaboration I improved the performance of a pipeline that utilises the software by 100,000 times compared to simply daisy-chaining existing software commands. This required an understanding of the scientific intent and the skill to engineer a high-performance implementation.
I would certainly like to elicit more collaboration around MRtrix3 by attracting more community contributions and by encouraging researchers to use the software as a development platform. However, I think this is difficult as the vast majority of MRtrix3 is written in C++, which is not a language that many researchers use. We’ve undergone multiple laborious back-end refactorings to arrive at an interface that expedites our own development. I believe it’s a great environment for developing and disseminating neuroimaging research methods, but it’s a tough sell for anyone outside of the core development team to adopt it as infrastructure for their own work.
At this point in my career, being selective regarding collaborations is both a privilege and a necessity. I’m attempting to persevere with a conventional research career whilst supporting a large and widely used research tool. While I enjoy many aspects of the latter, such a situation can become untenable for a researcher in the absence of explicit funding to support research software in its own right.
I am fortunate in that I am a fellow of the Australian National Imaging Facility (NIF), which supports the development and maintenance of MRtrix3 as part of the national imaging informatics infrastructure. Internationally we’re starting to see funding opportunities specific to research software (like the UKRI grant which allows our team to have a software engineer based in London). The conventional pathways for research funding here in Australia (NHMRC and ARC) do not directly support critical software.
What attracted you to maintaining research software over the years?
I don’t think that I ever made a conscious decision of “I’m going to maintain research software”. Once I began contributing to the software, it was natural to respond to issues and feature requests coming from the community. When you have a personal investment in software you develop a vested interest in ensuring it does what it claims, does it well, and expands in its capabilities. Unlike a conventional piece of research, where you contribute some small unit of understanding to a specific research domain, software is scalable – capable of facilitating a broad spectrum of research – which can give a greater sense of pride and impact.
I would also say that I’m driven to diligently maintain MRtrix3, given that I have first hand experience of what we called the ‘underbelly’ of open source science. In my haste to resolve a community request, I added a feature only for them to discover after journal publication that it was performing an erroneous calculation. This is nightmare fuel for research software engineers. That said, we tried to make the most of it: the affected researcher and I wrote a shared first-author publication to meticulously dissect my mistake, how it was detected, how we responded and rectified its effects on the (thankfully reproducible) scientific analysis. This shows the importance of explicit investment in software sustainment beyond the project that initiated it.
What do you see as the impact of the Eureka Prize for Excellence in Research Software?
It’s obviously great to have individual software projects recognised for their contribution to research, but for me the key impact of this award is the promotion of research software as a domain worthy of recognition. This prize is one of many steps to recognise software as a reportable and valuable output of research.
When research software is done well, and adopted broadly, it’s worthy of financial investment and recognition – contrary to the view that article and citation counts are the only measure of research success. The Eureka Prize for Research Software raises the awareness of the impact of research software in the scientific community.
Those of us involved with MRtrix3 have a history shared by many others: we became research software engineers before the term even existed. Some still view this as a trivial extension of research: you finish your experiment, you make your code public in whatever state it was in at the point of manuscript submission, and voila, you’re now a researcher and an open source software expert.
For research software to make a meaningful impact requires so much more. Supporting research software requires time and effort, a unique intersection of skills and persistent engagement with the research community – all of which can feel like an encumbrance. To have such efforts acknowledged and to attach a little prestige to this effort, is well deserved recognition I think.
Keep In Touch
You can connect with Rob via LinkedIn, GitHub and X/Twitter.
If you’d like to be part of a growing community of RSEs in Australia, become a member of RSE-AUNZ – it’s free!
“I’ve been to a couple of RSE-AUNZ meetups and would encourage anyone in this space to get to at least one in-person meeting. Many RSEs are isolated, don’t immediately see others undertaking roles similar to their own, and feel overworked and under-appreciated. Just chatting with others, finding the similarities and differences in your domains and personal experiences and engaging in a bit of catharsis can be self-reassuring. But do it out in the meat world if you can; it’s not the same as an avatar on a Zoom call!” said Rob.
ARDC-Sponsored Research Software Awards
The ARDC is proud to sponsor awards for research software and research software engineers in all stages of their careers. The goal of the awards is to strengthen the recognition of research software and those who develop and maintain it as being vital to modern research.
The ARDC continues to sponsor a wide range of research software awards for 2024.
Next month, we’ll speak to the MiniZinc team, another finalist for the 2024 Eureka Prize for Excellence in Research Software.
Also stay tuned for the announcement of the 2024 Ecological Society of Australia (ESA) New Developers of Open Source Software in Ecology award at this year’s ESA Conference, held in Melbourne from 9 to 13 December.
The ARDC is funded through the National Collaborative Research Infrastructure Strategy (NCRIS) to support national digital research infrastructure for Australian researchers.
Author
Reviewed by
Categories
Research Topic
Related Program
Related Projects
Related News & Events
- Finalists Announced for the 2024 ARDC Eureka Prize for Excellence in Research Software
- Announcing the 2024 Australian Museum Eureka Prize for Excellence in Research Software
- Shaping Research Software: An Interview with Anthony Truskinger
- Shaping Research Software: An Interview with Ben Foley
- Shaping Research Software: An Interview with Catherine Bromhead
- Shaping Research Software: An Interview with Cynthia Huang
- Shaping Research Software: An Interview with Dr Adam Sparks
- Shaping Research Software: An Interview with Dr Emily Kahl
- Shaping Research Software: An Interview with Dr Juan Nunez-Iglesias
- Shaping Research Software: An Interview with Dr Kate Harborne
- Shaping Research Software: An Interview with Dr Marcel Keller
- Shaping Research Software: An Interview with Dr Saras Windecker
- Shaping Research Software: An Interview with Fonti Kar
- Shaping Research Software: An Interview with Johanna Bayer
- Shaping Research Software: An Interview with Lydia Lucchesi and Sam Nelson
- Shaping Research Software: An Interview with Manodeep Sinha
- Shaping Research Software: An Interview with Matthew Sainsbury-Dale and Andrew Zammit-Mangion
- Shaping Research Software: An Interview with Melina Vidoni
- Shaping Research Software: An Interview with Michael Roach
- Shaping Research Software: An Interview with Roozbeh Valavi
- Shaping Research Software: An Interview with Ryan Wick
- Shaping Research Software: An Interview with Sharon Tickell
- Shaping Research Software: An Interview with Varvara Efremova
- Shaping Research Software: An Interview with the predictNMB Team
- Shaping Research Software: An Interview with Dr Juergen Knauer
- Shaping Research Software: An Interview with Professor Susanna Guatelli