Alessandro Felder is a 2025 SSI fellow and a Senior Research Software Engineer in the Neuroinformatics Unit (NIU) and in the Advanced Research Computing Centre at University College London. He is a core developer of the BrainGlobe Initiative, an open-source suite of tools to process, analyse and visualise brain microscopy data. He is also active in local and international community-building activities in bioimage analysis.

In this blog, I share the motivation for applying to the SSI fellowship programme, what the contents of my fellowship event were, what I’ve learnt during my fellowship, and how I think my fellowship activities fit into the wider landscape.

My fellowship event consisted of two "tracks" that formed part of Neuroinformatics Open Software Week—a larger event that I co-led with my colleague Niko Sirmpilatze (also a 2025 SSI fellow). I am deeply grateful to him and my other NIU colleagues for their support in making our vision into a reality. You can read our joint blog to know more about how we coordinated our fellowships, and our overall conclusions.

I would also like to thank my SSI mentor Richard Abel, who gave me some particularly helpful advice around how my fellowship could fit into my wider career plans.

Motivation—The Missing Bridge

I’ve spent the past decade of my professional life (as a PhD student, postdoc and then “official” Research Software Engineer) working at the interface between biological image analysis and research software engineering—both are fields that I have grown to care deeply about, and I like to share this enthusiasm with others.

During this time, I noticed various similarities in the community efforts in both fields: Research Software Engineers and Bioimage Analysts both see themselves as performing critical and underappreciated technical roles in the interest of scientific progress that lack appropriate career paths. The self-reported activities of a recent survey of bioimage analysts (see Supplementary Figure 1B of the preprint) overlap significantly with "the mixture of service delivery, research, innovation and teaching activities" cited in the job descriptions of generalist research technology professionals at UCL (e.g. for RSEs). There is even a recent paper which advocates for embedding software engineers in imaging facilities.

Despite these similarities, I was not aware of community initiatives that linked the two fields. I decided that an SSI fellowship event could help bridge the communities—in the hope that jointly advocating for recognition of technical roles in academia might result in better career paths for both.

As someone that works with whole-brain microscopy data, I was also aware that advances in imaging techniques mean imaging data is getting bigger, and that we need software that keeps pace with these developments. I also realised how important the perspective of bioimage analysts (here meaning anyone with a need to analyse imaging data, such as microscopy facility staff and early career researchers) is in addressing these software challenges. This was yet another reason to connect the specialist bioimage analysts with more generalist research software engineers.

One very awkward self-tape and an afternoon of interactions with amazingly collaborative people later, I was happy to find out that I was awarded the fellowship… and the real work began.

As I was planning the event, I decided to divide my fellowship event into a whole-brain microscopy data part, the BrainGlobe track, and a more general Big Imaging Data track with a focus on community and file formats. Participants could join just one track, or both.

BrainGlobe

In the BrainGlobe track, we strongly favoured applications where there was evidence for a clear immediate use for the BrainGlobe tools. We selected 15 applicants from around 50 applications—eight were based in London or Surrey, four were based in Europe and three came from further away (Singapore, USA, Australia).

The event itself consisted of hands-on BrainGlobe tutorials, a suite of open-source software tools for neuroanatomy I co-develop. BrainGlobe helps researchers process, analyse and visualise their brain microscopy data—an important datatype for my institute and a key application driving the need for software that can handle big imaging data. Participants were encouraged to bring their own data along. Fellow BrainGlobe core developer Igor Tatarnikov also helped a lot with this and led some of the teaching itself.

We were impressed with the level of preparation of the participants: many had brought their own data and detailed questions— and this led to the event being more of a two-way learning experience than we expected: we took note of 13 issues, mostly related to user experience or unusual setups, that we weren’t aware of. Two attendees went a step further and contributed improvements to BrainGlobe since attending.

We found this experience rewarding and highlighted the importance of a continued dialogue between users and developers.

Big Imaging Data

We selected 23 applications for the Big Imaging Data track—19 made it, with eleven attendees from outside the UK showing the global reach of the participants. Again, we were quite selective with the applications (we had space for 25 participants). I was particularly pleased to welcome four imaging facility staff, who I see as an integral part of the community because their role often includes training researchers on acquiring and analysing big imaging data.

The morning included an introduction and a hands-on tutorial around OME-Zarr, the "next-gen" community-centred big imaging data format. Designing these materials, I relied heavily on the open-source OME-Zarr for Big Bioimaging Data textbook, led by my colleague David Stansby and invited textbook co-authors Kimberly Meechan and Ruaridh Gollifer to present their work about benchmarking OME-Zarr libraries—thank you! I learnt a lot from them, and from designing the tutorial—a major take-away was that despite community support and a clear need for OME-Zarr, much of the software ecosystem around it is rather fragmented and immature, and more work needs to be done here.

In the afternoon, I introduced my personal perspective on the missing interactions between the bioimaging community and the RSE community—which was my motivation for applying for an SSI fellowship. We then transitioned into a speed-blogging session: I invited participants to discuss a related topic of choice in a small group and then write this up as a blog. I provided some possible topics as a prompt, but participants were free to come up with their own. This resulted in four blogs (in preparation), which centred around career paths, the notion of open science, guidelines for using OME-Zarr and bridging communities.

I was very inspired by the level of buy-in from all participants, especially for the speed-blogging session and I am excited to see our blogs published. Going beyond learning technical skills and into community building was an important part of my plans— and while the community-building aspect was built-in throughout Open Software Week, this part let us explicitly think about and imagine the communities we want to be part of.

It was also great to see an OME-Zarr-related hackday project. We started writing jupyter notebooks that showed how different libraries can be used to convert datasets to OME-Zarr.

The bigger picture

My hope is that my fellowship event was a small step in coordinating technical development and career paths in both fields. I believe it was a timely step, too: for example, the Global Bioimage Analysts' Society is aiming to include software developers in their scientific advisory committee.

My fellowship made me realise how interested I am in seeing where domain specialists and generalists meet, and how this helps drive research forward. I see this as a key area of growth for the Research Software Engineering movement, and we need to find solutions to include more people from domain-specific backgrounds.

Leading this event also helped me become more visible in my communities—alongside my SSI fellowship, I have helped organise the upcoming Crick Bioimage Analysis Symposium, which will feature a panel discussion around software sustainability and funding (kindly supported by the RSE Society) and I am also involved in organising the data session of a university-wide bioimaging conference. Finally, BrainGlobe was recognised with an Open Science prize recently.

I look forward to the next iteration of the BrainGlobe and Big Imaging data tracks next year!