Recently, I got the chance to attend Open Data Camp 10 (ODC10) for the very first time! The event took place on 27–28 September 2025 at the University of Edinburgh Business School. It was an unconference style, which meant the event agenda was driven by the people, for the people. Each morning started with a pitching session where anyone was welcome to share their elevator pitch idea (in just 30 seconds!). All the ideas were then put up on a big board (colourful sticky notes!), and everyone was free to choose the topic they wanted to be a part of. I pitched something too, more on it later in the blog.

Image: (Left to right) Morning welcome and pitching sessions, session grid for day 1.

One of the discussions that stood out for me was on Maturing Open Data. I liked the idea of treating data like a product, something that has versions, documentation, and dedicated roles like analysts and lawyers. There was also discussion about platforms like Hugging Face for AI and how something similar could exist for data. In another session, there was a discussion on how to convince senior leaders to support open data policies, which made me think a lot about the different skills needed at different stages.

Image: (Left to right) Morning welcome and pitching sessions, session grid for day 1.

There were some big-picture policy discussions too. One of them was about the UK’s plan for a National Data Library (NDL), with the idea of having a single federated place to store and access data. Another one was on Digital IDs, where the participants were asked to think about it both as citizens and as data professionals. This made the discussion really interesting.

Unicorn Mandala art session

I pitched and ran a hands-on creative session called “Drawing Parallelism: A Unicorn Mandala Art Workshop on Open Data and Collaborations.” For this session, the participants were divided into three teams and I provided mandala kits to everyone so they could collaboratively create a unicorn design, chosen to honour Scotland’s national animal. My inspiration was simple: just as a mandala is built from many shapes and colours, the open ecosystem is built from many contributions. No single piece stands alone, but together they form something beautiful and meaningful.

Image: sketch from Drawnalism Pvt. Ltd.

As people coloured, we reflected on how this connected to open data and collaboration. Some participants approached it like their day-to-day work, for example, starting with the “infrastructure base” of the unicorn. Others experimented with by trying different colours and asymmetry, some chose non-convential colours for the rainbow, and while others kicked off with a group chat about colour schemes. Some joined in later, just like how people can enter a project midway. A few filled entire sections at first but then shifted to patterns like dots and lines, showing how approaches evolve over time. We even had binary 1s and 0s added outside the design to represent data, and others added entirely new elements of their own.

Image: Unicorn mandala art work pieces created by three teams.

When teams swapped their mandalas, keeping the same pens but working on someone else’s design, the dynamics shifted. People noticed it was harder to feel invested in a project they hadn’t started, and some worried the original team might disapprove of their additions, echoing real fears in collaborative projects. Yet, over time, new ideas emerged: like patterns, reflections on perspective (how the colours stayed even when the lines disappeared), and new layers that blended with the old. These discussions beautifully mirrored the challenges and joys of open collaborations: ownership, trust, creativity, and seeing projects evolve beyond their original intent.

Check out the session slides.

Image: (Left to right) Udon bowl at a restaurant, a picture of me in the autumn of Scotland.

What I really loved about the event was the freedom to move around thanks to the “Law of Two Feet: If a session didn’t feel meaningful to you, you are welcome to join another one”. There was also a fantastic team from Drawnalism who created live sketch notes of the sessions. As this was my first Open Data Camp, I was struck by how friendly, collaborative, and creative it was. Walking away from Edinburgh, my big takeaway is that open data is not just about technology, it’s about people, culture, trust, and creativity!

Get In Touch:

Email: bhogaljyoti1@gmail.com
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I was happy but surprised at the offer of an invited talk slot at 2025’s HPC-AI Advisory Council Annual Conference, hosted by SFTC DiRAC, on my SSI Fellowship theme of “Better Hardware, Better Research” - applying the principles of open source software to hardware, specifically in environmental science. The theme was “Trustworthy computing at a range of scales”; talk of open source microsystems feels a world away from massive HPE supercomputing clusters. But I gamely went along, and really enjoyed the event. The rest of this post is a condensed summary of the talk.

This picture is the best credential I’ve got to offer - 20 years ago, on the right in the green t-shirt, at Map Limehouse, coordinating the first OpenStreetmap mapping party. I may not have changed much, but the tech looks pretty retro now!

I got involved with OSM through local community wireless networks. These were the days before home broadband was widespread, or "smart" phones existed. A network of idealistic artists and hackers set up consume.net, then later Wireless London; our London Free Map project which got folded into OSM was a spin-off from that.

I was a software artist then, but I'm a "Research Software Engineer" now, working my way through different kinds of land survey organisations to end up at the UK Centre for Ecology and Hydrology. UKCEH has some lake environmental monitoring projects continuously in place since the 1940s! Monitoring work takes in atmospheric chemistry, air and water quality, biodiversity, and land use change. It's field samples, lab-based work, and electronic monitoring, as well as a lot of modelling.

UKCEH also hosts an Engineering Workshop, a kind of in-house hackerspace where a group of engineers collaborate with researchers on prototypes. Their best inventions aren’t electronic - like this river flume, designed neither to float or sink, that collects algae on ceramic plates infused with different chemicals. There are training courses in developing and debugging field electronics and sensors

There are "pockets of excellence" whose work is either inspired by open source hardware (the AMI+ system, a setup similar to the open source MothBox and growing some elements of the AudioMoth) or directly reusing it (bioacoustics surveys using the MicroMoth). Colleagues follow the progress of open source research hardware projects with intense interest, motivated by the potential of AI-assisted research - automating manual tasks, or aggregating many data sources to analyse whole landscapes or soundscapes.

But for larger infrastructure projects, the organisation still buys in proprietary dataloggers and devices. A few months after I joined UKCEH, I sat in on a project kickoff meeting, wondering why research hardware wasn't being considered in the same way as research software - open, collaborative, reproducible at minimal cost, with funder incentives to do so.

When the Software Sustainability Institute announced its call for Fellows for 2025, and a colleague encouraged me to apply, I didn’t have to think very long about the theme. I proposed to coordinate a series of workshops bringing together field researchers with hobbyist hardware hackers. I enlisted Libby Miller as a collaborator, bringing their model of participatory, hands-on, community-oriented “social invention” developed at BBC R&D.

I was full of visionary optimism, and soon discovered not only how much I don't know, but how much prior art and groundwork has been done. I want to highlight the work of Julian Stirling, the founder of the Open Flexure high resolution microscopy project. They say it all in Open instrumentation, like open data, is key to reproducible science. Yet, without incentives it won’t thrive. 

Open Flexure is redistributed in the UK by Labcrafter, a startup founded by Margriet and Gerrit Nielsen, focused on open research hardware. It was when I read that Open Flexure had been supported by the NLNet fund for next generation internet infrastructure that I got an inkling of why my talk had been welcomed by the HPC-AI Advisory Council.

The work of the Open Source Hardware Association is essential here. The OSHWA certification programme offers a hardware equivalent of the Open Definition for data. If it’s OSHWA-certified,is reproducible and reusable without constraints.,

As an RSE, exploring hardware is a route away from "stick a camera on it" solutions, and approaches that reuse image deep learning architectures. To ask the same questions, gather the evidence, act on the answers, in ways that don't need as much data, storage, bandwidth, power or scale. 

I’m also seeing from the perspective of the art practice of locative social media in the 2000s. The idealised future of "locative, ubiquitous and pervasive computing" has become a behaviour modification surveillance infrastructure. As technologists, it’s on us to plan for a built-in resistance, to consider whose hands our work could end up in, how it could be used. 

The tendency to foresee the unexpected negative applications of new inventions put me off doing any creative technology work for a long time. I definitely have a tendency towards terrible inventions. This is one of my most least-favourites: a dog backpack LoRaWAN gateway/aggregator. The dog's going for a walk and gathering at the trees where its peers gather anyway. Why not collect and deposit telemetry on the way? As terrible inventions go, #dogtech relatively benign.

I'm inspired by the recent work and speaking of Dan McQuillan here, on the topic of "Decomputing" - Decomputing takes the idea of ‘computing within limits’ to refer not only to the scale of computational machinery but to limits of extractive and colonial logics, limits to a biosphere’s ability to recover, limits to our Western knowledge systems and limits to tech solutionism… rejection of scale as a heuristic for the way forwards".

As Libby Miller writes, "Change comes from coalitions of groups with the same interest" - but when you're interested in so many things, how do you find the smallest core of shared interest to move forward from? I visited the Gathering for Open Science Hardware to learn. And there are so many different kinds of interests there! Folks working on genomics, on lab instruments, in materials engineering. Glimpses of untapped potential for fundamental change in how we react to and modify our environment, at a scale that's hard to take in.

I wanted to end the talk on an up note, so offered this - the RC2014 Mini II Picasso. It's an open source hardware art project that was launched as an April Fool's joke that's also a shippable product serious. A beautiful piece of retro hardware design by a practitioner with a loyal interest community, a project full of joy and care. (I'm still halfway through building mine - I solder slowly!) For me, Open Source Hardware is as essential to joyful art computing, as much it is a conceptually essential part of Digital Research Infrastructure that supports open and collaborative science.

Introduction

The core goal of my SSI Fellowship is to facilitate knowledge exchange of skills and competencies between humanities and sciences. This includes improving my own knowledge and skills relating to the latest AI techniques and their relevance for teaching and learning.

In November 2025, I attended the ELIXIR BioHackathon Europe event at Bad Saarow near Berlin, Germany. The BioHackathon runs every year thanks to ELIXIR Europe and provides space for collaboration and innovation in computational biology and bioinformatics. Participants engage in intensive, hands-on programming and content-creation activities, data integration and software development. I joined the project ”Knowledge graphs for metadata on training”, led by Geert van Geest (SIB Swiss Institute of Bioinformatics), Harshita Gupta (SciLifeLab Sweden), and Vincent Emonet (SIB).

Outputs, report and user stories

The project has published a report of its outcomes on BioHackrXiv [precise link and citation to follow]. Highlights of the report include:

• A description of what a knowledge graph is, and how this structured data representation can greatly facilitate complex querying and applications to deep learning approaches like generative AI.
• A description of the training registry metadata sources we used (TeSS and Galaxy Training Network) and the most important metadata fields.
• A description of the code written to build the knowledge graph, and Model Context Protocol (MCP) server we developed that exposes a suite of tools for searching and querying training materials. 

Several projects at the BioHackathon featured Model Context Protocol (MCP), and this was a new concept for me. MCP is an open standard produced by Anthropic (the company responsible for Claude); think of it as a more powerful kind of API. An MCP server gives AI agents a consistent way to connect with data, tools and services, while reducing hallucination. Agents can perform multi-step tasks, reducing the effort for the user who can interact via a natural language interface. For us, we can present a LLM chat bot that can query multiple training registries at once and provide answers to much deeper questions.

When I applied to this project, I had intended to work on the Python code directly. In the end, I changed my focus to provide project and community management. My most significant contribution to the project was to lead the development of 11 user stories. These user stories are a representative selection of the kinds of queries a user might make of the system, following a popular format:

• As a [user persona]
• I want to [do task]
• …so that [outcome/benefit]

An example user story we created is:

• As a bioinformatics scientist
• I want to define a learning path of training materials and/or events
• …so that I can become a specialist in artificial intelligence within the following specified time and resources: I have 6 months, a workload of 14 days, I live in Sweden and I can travel within Europe once.

Having a range of user stories ready to refer to throughout the project helps the developers to keep the requirements in mind when coding and allows them to focus on the software development.

Impact and opportunities

The project was a successful creation of a proof-of-concept for the ELIXIR ecosystem and beyond. There is a promising possibility of MCP for scientific applications, where used in combination with a LLM, to allow for natural language querying while including information from a trusted resource.

Participating in the BioHackathon gave me a better appreciation of current AI applications and features, in turn supporting me in my core work and with other aspects of my SSI Fellowship. I learned more about the importance of having persistent, unique identifiers for all nodes in a knowledge graph, and how it is valuable for various concepts described within the source materials to be described with an ID. The knowledge graph we built had gaps which had to be filled afterwards, and it would be more accurate if these gaps were already filled by the training providers before we scraped the training materials. We already associate the URL of a training course or event as the unique identifier for the material as a whole, but what about the trainers, the hosts and the locations of events? There are recommended authorities to consider, such as ORCiD for persons, ROR for organisations, and Open Street Map for places. I can now advocate for training registries and providers to host additional metadata for these inner entities within a given training material.

Thank you to the project leaders Geert van Geest, Harshita Gupta, Vincent Emonet, and all the other project members Finn Bacall, Jerven Bolleman, Jacobo Miranda, Dimitris Panouris. Thank you also to the people who kindly helped answer my questions during the hackathon: Alex Botzki, Eli Chadwick, Alban Gaignard, Helena Schnitzer, Ginger Tseung, Bérénice Batut, Carole Goble.

Figure 1. Scientific fields converging on computer-vision-based methods for quantifying behaviour. Deep-learning approaches extract user-defined body parts directly from video without markers, enabling high-throughput, non-invasive motion tracking across species.

Overview

Niko Sirmpilatze is a 2025 Software Sustainability Institute (SSI) Fellow and Senior Research Software Engineer at the Sainsbury Wellcome Centre, a neuroscience research institute affiliated with UCL in London. He builds open-source tools to study brains and the behaviours they produce, and leads movement—a Python package for analysing animal motion.

I organised the first Animals in Motion workshop in London, which was the central goal of my Software Sustainability Institute (SSI) Fellowship. The event brought together early-career researchers from diverse disciplines, all united by a shared aim: quantifying animal behaviour using open-source software.

Animals in Motion formed part of a broader Open Software Week held on 11–15 August 2025, which I co-organised with SSI Fellow Alessandro Felder, supported by many of our colleagues at the Neuroinformatics Unit. You can read more about the wider week in this companion post, where Alessandro and I reflect on the added value of combining our Fellowship activities.

In this post, I share highlights from the Animals in Motion workshop, reflect on what we achieved, and outline what comes next. Throughout, I use “we” to refer to the full team behind Animals in Motion—including Sofía Miñano and Chang Huan Lo, who were instrumental in designing, developing, and delivering the workshop materials.

Fellowship goals

When proposing my Fellowship project, I argued that several scientific fields interested in animal behaviour—from neuroscience to behavioural ecology—are converging on shared, computer-vision-based methods for measuring motion. Thanks to advances in machine learning, researchers can now track body movements directly from video, at scale and low cost (see Figure 1).

I saw this convergence as an opportunity to bring together researchers from these diverse communities and train them in using sustainable, open-source tools that support their common workflows. The goal was to build bridges between these communities and to create a two-way exchange between researchers and tool developers:

• Researchers would gain theoretical grounding, practical skills, and a new peer network.
• Tool developers (including the organising team) would learn from real users, building relationships and gathering feedback to guide future work.

By blurring the lines between these groups we hoped to consolidate and strengthen the shared ecosystem of open tools for behavioural analysis.

Workshop attendees

We promoted Animals in Motion widely across social media, mailing lists, online communities, and Slack channels, as well as through targeted outreach to graduate programmes and institutes focused on animal behaviour. As this was the first event of its kind, we were unsure how much interest it would attract. The response exceeded all expectations: we received 60 applications from around the world, most of them of high quality.

We selected 25 participants, the maximum number we could accommodate for hands-on teaching, and were delighted that 24/25 attended both workshop days—dispelling our concerns about potential no-shows. Thanks to support from the SSI and our other funders—described in the companion post about the Open Software Week post—we were able to charge no registration fees, provide catering for all, as well as fund travel for four Animals in Motion attendees. This helped us achieve strong geographic diversity: 9 attendees from London, 7 from the rest of the UK, 6 from Europe, and 2 from India.

We succeeded in bringing together diverse disciplines, species, and experience levels. Based on an opening poll (Figure 2), we welcomed researchers working with animals ranging from mice to… “flying” frogs—and spanning fields including neuroscience, behavioural ecology, biomechanics and conservation. Career stages ranged from Master’s students to early-career principal investigators. Two-thirds of attendees identified as women, likely reflecting the underlying demographics in these fields.

Figure 2. Word clouds generated using mentimeter.com show the range of scientific disciplines and model species across attendees.

From both direct observation and participant feedback, this mix of varied backgrounds and shared technical interests worked extremely well. Engagement levels remained high throughout the workshop and participants felt enriched by the diversity of attendees.

Workshop content

We began the workshop with a primer on deep learning for computer vision, in which Sofía Miñano introduced the concepts and technologies that underpin modern animal tracking tools. Several participants appreciated the accessible introduction to what can often feel like a complex and opaque field.

In the afternoon, we switched to practical training with SLEAP, using materials prepared by Chang Huan Lo. Participants learned how to annotate videos, train computer vision models, and use them to track animals. We provided sample videos to ensure everyone could follow along, although some people experimented with their own data, resulting in a fun showcase of diverse animals.

Day two focused on analysing motion tracking data using our open-source Python package movement. Participants worked through exercises that introduced them to loading, cleaning and visualising data, as well as asking questions about the animals’ kinematics. We finished with two real-world case studies that demonstrated how the tools covered in the course support ongoing scientific research.

Catering to the wide range of coding experience among attendees proved to be a challenge, especially during the Python-heavy second day. We had offered an optional introductory Python session before the workshop, but that could only go so far. To address this, we encouraged more experienced coders to support classmates, which had the added benefit of contributing to a strong sense of community.

Participants told us they would have appreciated even more time for exercises and discussion, and that is something we are keen to build into future editions. It was also extremely rewarding and useful to see our movement package in action, crash-tested in the hands of so many users.

We have chosen to openly share all workshop materials in the Animals in Motion Online Handbook. The handbook contains chapters written by Sofía, Chang Huan and myself, and it can be followed independently as a self-paced resource. We intend to keep expanding and updating it in response to feedback gathered during the workshop, so that it remains a freely accessible and reusable teaching tool for the community.

Blurring the lines between users and developers

A healthy open-source ecosystem relies on helping users become contributors. Hence a key aim of my SSI Fellowship was to give animal behaviour researchers the skills and confidence to take that step.

The Hackday, held on the final day of Open Software Week, was our main way of putting this into practice. About half of the Animals in Motion participants stayed on, joining attendees from other tracks of the week. To help everyone get started, we preceded the hackday with an optional half-day workshop on Collaborative coding with git, delivered by Joe Ziminksi and Laura Porta.

The hackathon itself followed a format inspired by the SSI Collaborations Workshops. You can browse the projects on this board. Some teams explored open-source tools using their own data, while others made contributions upstream—including several pull requests to movement, two of which have already been merged. One participant, Carlo Castoldi, also wrote a blogpost about his contribution, published on the movement website.

I will take this opportunity to especially thank Sofía Miñano, who proposed no less than five project ideas, mentored multiple teams during and after the hackday, and helped Carlo with finalising his contribution. She was the true hackday hero.

What's next

Organising and leading Animals in Motion has been the most rewarding experience of my professional career. I’d had ideas like this floating around for some time, but the SSI Fellowship was the catalyst that turned them into something real. The process of articulating those ideas for the Fellowship helped give them structure, and feedback from colleagues—as well as from my SSI mentor Colin Sauze—further refined them into a concrete plan.

I’m excited to keep building on this work. It’s been wonderful to see Animals in Motion so warmly supported by my team and our host institute. Animals in Motion will return on 17–21 August 2026, as part of the Neuroinformatics Unit Open Software Summer School—an event we aim to make an annual tradition.

My hope is for the workshop, alongside its online handbook, to form the nucleus of a growing community of practice for open-source tools in animal behaviour. In the long run, I’d love to see other teams around the world running their own versions of the workshop, building on the open materials we’ve created. If you would be interested in supporting such an effort, I'd love to hear from you. You can find my contacts through nikosirmpilatze.com.

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!

Alessandro Felder and Niko Sirmpilatze are both 2025 SSI Fellows and Senior Research Software Engineers at the Sainsbury Wellcome Centre, a neuroscience research institute affiliated with UCL in London. Alessandro is a core developer of the BrainGlobe Initiative, an open-source suite of tools for processing and visualising brain microscopy data. Niko leads movement, an open-source Python package for analysing animal body movements from video.

Overview

In August 2025, we co-organised the Neuroinformatics Unit Open Software Week (OSW) a five-day event that brought together 44 attendees from 12 countries across four continents to learn open-source approaches for handling large imaging datasets, processing whole-brain microscopy data, and analysing behavioural videos. OSW emerged by combining our SSI Fellowship plans into a single, larger initiative.

Across the week, 13 speakers delivered seven sessions, grouped into three main tracks supported by four shared satellite events:

Schedule of the Neuroinformatics Unit Open Software Week.

Main tracks

• Animals in Motion focused on open-source tools for tracking and analysing animal motion from video.
• BrainGlobe consisted of a hands-on introduction to open-source tools to process, analyse and visualise brain microscopy data.
• Big Imaging Data featured introductory technical tutorials and a community session around big imaging data formats and libraries.

Animals in Motion was led by Niko, while the other two tracks were led by Alessandro.

Shared satellite events

• Introduction to Python — optional one-day refresher for participants wanting to strengthen their programming foundations ahead of the technical sessions.
• Careers Clinic — a panel discussion with five Research Technology Professionals from life sciences, highlighting diverse career routes and opportunities.
• Collaborative Coding with Git — practical guidance on version control and contributing to projects on GitHub.
• Hackday — a dedicated day for participants to collaborate on small projects, drawing inspiration from the SSI’s Collaborations Workshops.

The programme was supplemented by a series of diverse social events in the evenings, including a walk in the Regents Park, an Irish folk music jam session, a neuroscience-themed pub quiz, and a creative live-coding evening.

In the two companion blog posts, we describe the individual training tracks we led and how they helped advance our respective Fellowship goals.

• Bridging communities around big imaging data for brain microscopy and beyond

• Animals in Motion: empowering behavioural researchers with open-source tools

In this post, we reflect on the experience of joining forces to achieve something more ambitious than either of us originally envisioned. We share how the event came together, the synergies that shaped it, and our plans for the future.

Synergistic fellowships

Open Software Week wasn’t part of our original plan. We had each proposed independent Fellowship projects and were simply lucky that both were funded in the same cohort. The idea to combine them came to us later. It made sense — we work side by side at the same institute and had already planned to use the same spaces for our respective events. We expected that we could combine some parts of our events, such as the hackday, and share the logistical and administrative burden. To our surprise, joining forces came with other unforeseen benefits, too!

We didn't expect how much working together would help us when we needed someone to bounce ideas off, or someone to hold us accountable for getting things done (including writing this blog post!).

We also benefited from each others' and our line manager Adam Tyson's perspective as we reviewed an overwhelming amount (~120) of high-quality applications. We were limited to 50 participants - the maximum number we could teach hands-on in our space. It was a lot easier to make tough decisions together. It helped that Niko wasn't as emotionally close to Alessandro's plans, and vice-versa. Adam could tie-break and keep a higher-level perspective.

Making our fellowships into a larger event with existing seed-funding allowed Adam to secure additional sponsorship for OSW. We got small grants from the Society for Research Software Engineering and AIBIO-UK, as well as support from our host institute. The Sainsbury Wellcome Centre provided funding for OSW in addition to their already generous in-kind contribution of administrative support and provision of teaching rooms. This enabled us to provide catering throughout the week, not charge registration fees and support eight participants with accommodation and travel costs.

Attending tracks on different topics did not prevent our participants from making friends during the shared breaks and social events. The boundaries between our events were fluid and we were happy to see many engaging interactions: a participant switched tracks at the last minute, an Animals in Motion attendee helped with BrainGlobe problems during the hackday, and a few participants took time out of the Big Imaging Data event to attend the Careers Clinic.

Although OSW grew out of our SSI Fellowship initiatives, it was quickly and enthusiastically adopted by our fellow research software engineers in the Neuroinformatics Unit. A final positive outcome was that organising and leading OSW (it was pretty intense, to be honest!) brought us closer together as a team. The end of the week found us having tea and biscuits together, exchanging stories and cooling down from all the excitement.

What made Open Software Week a success

OSW was rewarding and worthwhile for us organisers, and we hoped that the participants would share this experience. Gratifyingly we received overwhelmingly positive feedback; we've included some anonymous excerpts below.

Sparked a bit of a eureka moment after months of agonising over how to analyse my data!

My whole PhD feels doable now!

The heterogeneity of the attendees was truly enriching.

Atmosphere was very friendly and down to earth.

The communication and offers of help were incredibly kind and respectful. I felt uninhibited to ask questions, which I don't take for granted!

It was incredibly valuable to learn directly from the developers and share the space with researchers from across the field.

I thought the motivations behind the week and the organising team were eye-opening as to how to make a career supporting research and doing this type of work. I didn't expect to feel as welcomed and motivated to keep going in this field…

Moreover, we had little to no decline in participation as the week progressed. Attendees, including the locals, kept showing up for all the days they'd signed up for. Many of them remain engaged on our public discussion forums and some have already contributed multiple times to our open-source tools. One of our participants, Marco Dalla Vecchia, wrote a first-hand account of his experience, which you can read on the Neuroinformatics Unit website.

We have been reflecting on what made this event such a success.

One factor that stood out was our model of combining domain-specific data analysis training with general good research and software practices. Because participants were already motivated to learn skills they could immediately apply in their own work, they were more engaged and receptive to topics that can otherwise seem dry, such as version control or introductory Python. We think this integrated approach may be more effective than teaching software skills in isolation. Our selection process also reinforced this, as we prioritised applicants who were likely to make immediate use of the tools and methods covered.

We also made a concerted effort to create a welcoming and informal atmosphere, using techniques from SSI Collaborations Workshops and other communities with a similar ethos—like Brainhack. Each day started with a welcome session, where everyone was reminded to follow the Code of Conduct, be collaborative and respectful, make friends and have fun. We encouraged participants to follow the Pacman rule and tried to lead by example on that. We also made sure to include unconference-type sessions with participant-led co-working activities and provided an online platform for people to chat during the event.

Looking ahead

We plan to build on the success of OSW by growing it into an annual summer school. Next year's event is scheduled for August 17th-28th 2026 and registration opened on December 1st 2025.

We aim to expand the programme to two weeks. This will allow us to introduce a dedicated additional track on electrophysiological data, an important neuroscientific modality that was missing in 2025. The 2026 event will also provide more opportunities for participants to present their work and have more time for collaboration.

To ensure long-term sustainability, we will shift to a mixed funding model that combines sponsorship with registration fees, while continuing to offer travel support for participants from under-resourced institutions and countries.

We are excited to host our next cohort in London next summer!

Acknowledgments

Looking back, OSW feels like the most impactful initiative we have undertaken so far. Experiencing how our efforts helped connect researchers across disciplines and career stages was deeply fulfilling. We are grateful to everyone who helped transform our initial fellowship ideas into something far greater.

We wish to thank all of our colleagues in the Neuroinformatics Unit. Shout-out to Adam, Chang Huan, Igor, Joe, Laura and Sofía, who all contributed in multiple ways, from developing and delivering training materials, to organising social activities and leading hackday projects.

OSW would not have taken place without the generous funding from the SSI, the Sainsbury Wellcome Centre, the Society for Research Software Engineering and AIBIO-UK. The finance teams at SSI and the Sainsbury Wellcome Centre also helped streamline the admin and ensured we never had to cover costs out-of-pocket. Our Events Manager Karen Fergus was instrumental in arranging room bookings and, crucially, managing travel and reimbursements for the eight stipend recipients. The food provided by the catering team received frequent praise in participant feedback, and the security team supported us with room set-up and access throughout the week.

We extend our thanks to our panelists — Mayo Faulkner, Vicki Yorke-Edwards, Laura Porta, Jonas Hartmann, and SSI Fellow Batool Almarzouq — for generously sharing their time and career insights with participants.

Finally, we appreciate the contributions of those who brought creativity and fun to our social events. Jesse Krichefski and Ryan Cini prepared questions for our pub quiz, and the creative group pastagang performed live-coded music and visuals in a collaborative jam with OSW participants.

The most important people to thank are the participants themselves, who trusted us with a week of their time, and contributed not only intellectually, but also by shaping a positive and supportive atmosphere. We are greatly enriched by our interactions with them, and we hope they were too.

Event info:

For the first week of June 2025, I was at the ELIXIR All Hands meeting in Thessaloniki, Greece. ELIXIR is an intergovernmental European life sciences infrastructure with members from over 240 research institutes in 21 countries. All Hands is an annual event bringing together members of the ELIXIR community and partner organisations from across Europe to review ELIXIR’s achievements, ongoing activities and future plans.

This year was the 11th annual meeting - my 3rd All Hands. The event was full of opportunities to build networks and community, as well as learn about inter/national successes and challenges to anything life science infrastructure related. I was also there as a participant in the second cohort of ELEAD, ELIXIR’s leadership and diversity mentoring programme to support women’s leadership growth in ELIXIR.

Pre-All Hands:

I flew to Thessaloniki early to attend a networking dinner and peer-mentoring workshop as part of the ELEAD programme. This was the first time our ELEAD cohort met in person, along with the ELEAD programme team and our trainer, Louise Schubert. We had a lovely dinner on the Sunday evening, full of good food and positive connections with my female colleagues.

The next morning, we were all up bright and early for our workshop. Starting with an introduction to peer mentoring and how it is set up for ELEAD, we formed our peer mentoring groups, an essential part of ELEAD. Throughout the programme we meet regularly in our groups to reflect on our own professional practice and support each other through career successes and challenges. It’s a very rewarding part of ELEAD and I felt right at home with the rest of my group - being honest about things we have been finding difficult at work quickly brought us close together, and I left the workshop feeling a lot of inspiration and gratitude.

All Hands:

Day 1:

Then it was time for the main event! Which importantly started with lunch.

As always, the first session was opening remarks from the host node (Greece) followed by a keynote from Naveed Aziz, Vice President of R&I at Genome Canada, who covered infrastructure and governance similarities between EU and Canada and an interesting overview of the past 25 years of Genome Canada. 

After a coffee break, it was time for the first parallel sessions. I went to the mini-symposium on Cross-border Access to Human Genomes and Linked Data at Scale. This session covered advances in European genomic data infrastructure, including federated infrastructure and its practical barriers, and a walk through of how ELIXIR is involved with the European Cancer Mission, before ending with a panel discussion. The day ended with a very busy poster session and welcome drinks at the venue.

Day 2

The second day kicked off with 2 back to back parallel workshop sessions. I first attended the workshop on Enhancing RDM Resources led by the ELIXIR RDM community. After a brief introduction, we discussed various RDM topics, from incentives, physical data needs, and RDM training for overlooked professions.

Then I went to the workshop led by the ELIXIR Cancer Data community, Trends in Services for Cancer Research. Here I learnt a lot about cancer data (I work with musculoskeletal data but we covered a lot of relevant topics such as multi-omic data integration), as well as standards such as DOME for improving trust in AI.

There was then a 90-minute lunch & networking break - a great chance to catch up with international colleagues and have a more in-depth look at the posters when it’s less crowded. It was then time for the second plenary, Global Collaborations: Perspectives from Research Infrastructures, with representatives from Euro-BioImaging, Instruct-ERIC, and the ELIXIR Staff Exchange and Global Engagement initiatives. One set of flash talks and fascinating panel discussion later, I had a much better idea of the achievements, challenges, and opportunities that come with large international collaborations.

Another coffee break, then the final parallel session of the day - 3 mini-symposia on biodiversity data, empowering knowledge sharing, and node and people development. I skipped this session - it had been an intense 2 days so far and I needed a break if I was going to make it to the end! The evening ended with the ELIXIR-UK node dinner, unsurprisingly as we’re in Greece there was amazing food, a great chance to catch-up with UK colleagues.

Day 3

It was again a jam packed day of workshops, a plenary, and symposia. First, I went to the ELEAD workshop where we heard about other leadership initiatives for women in infrastructure in Europe and beyond, before a very interactive session mapping all initiatives we knew of and reflecting on which ideas could be useful for us to put into practice.

Then I sat in the ELIXIR & EOSC workshop, an important and exciting discussion around the future development of EOSC nodes, how they’re structured and linked with ELIXIR, and how to stay up to date on EOSC developments and strategy. I came away with more knowledge of EOSC than the year before but still a bit confused - initiatives as big as EOSC are hard to get your head around!

There was then a long lunch/networking session, where I met my ELEAD mentor for the first time. Another key part of ELEAD is being paired with a senior mentor to support your career development - it was exciting to finally meet each other and start this process. There was another plenary on ELIXIR Node Roles, Services, and Connections, an informative session from the ELIXIR Hub and several national nodes on the different node coordinator roles and how the nodes and ELIXIR hub interact and engage on various projects and services.

The final session of the day I went to was on Federated Service Delivery: Enabling Sensitive Data Computing in ELIXIR, covering the complex additional needs of sensitive data, what projects are working on this in ELIXIR, other domains we can learn from (e.g. climate data), ending with a discussion on all the above and what is needed to federate compute services in ELIXIR.

The day didn’t end there! That evening was the conference dinner at another venue in Thessaloniki. We had a nice drinks reception overlooking the sea before heading inside for a delicious meal accompanied by a fantastic display of traditional Greek dancing and music. 

Day 4

The final day had sadly arrived. Again, it kicked off with parallel workshop sessions - I went to a very engaging workshop on Data Annotation and Representation delivered by colleagues from the University of Nottingham. After a brief introduction to the workshop, we were split into two teams, debate style, to argue for or against the contentious statement: “All annotated datasets are unreliable”. We had a lot of interesting discussions in our teams before a fun debate at the end.

A quick pit-stop for coffee and then the closing plenary session. Irene Papatheodorou gave an insightful talk on her work on phenotypes at the Earlham Institute, and then we heard an overview of ELIXIR’s 2026 plans before poster prizes were awarded. The session ended with the most anticipated slide of the meeting, where is next year’s All Hands? [Drum roll] Lyon, France!

Lunch was a final chance to say goodbye to colleagues before heading back home. It was a fantastic All Hands as always, and although I was very exhausted from an intense 4 days of networking and new information, I left feeling very connected, inspired, and full of ideas. Until next year.

Slides, posters, and an event report from ELIXIR All Hands 2025 are available to all.

Thank you to the Software Sustainability Institute for funding my accommodation for this meeting.

The first DisCouRSE Focus Group: Team Culture and Leadership in dRTP contexts will take place Monday 19 January at King's College London.
 

This year, Reuben College hosted the third Dx4LMIC Conference, bringing together students and professionals from engineering, medicine, policy, and more. The event offered participants a chance to share insights and experiences from their respective fields, with a focus on the challenges and opportunities of improving medical diagnostics in low- and middle-income countries (LMICs). It was the biggest conference the college has hosted so far, with around 110–120 attendees. The event was very popular and we had to close registration early and start a waiting list. 

Across the two days (plus a pre-conference data science workshop), speakers shared insights on a wide range of cutting-edge tools and ideas, from using machine learning to transcribe patient histories, to bioengineering techniques that allow multiple PCR reactions to run in a single well, significantly reducing cost and complexity. We also heard about AI models trained on pulse oximeter data to help detect early patient deterioration in Vietnam, showcasing how diagnostics and digital health are converging in real-world settings. The day before I also ran a pre-conference technical workshop on data-centric approaches to learning machine learning.

Talks on responsible modelling and evaluation were a particular highlight this year, reflecting one of the conference’s key themes. Dr Fu Siong Ng spoke about the value and complexity of clinical data from LMICs and the importance of using such data responsibly. He introduced a method for diagnosing Chagas disease directly from over 2 million ECGs collected from Brazilian patients. We also heard from Reuben’s own James Anibal, who shared the practical challenges of deploying machine learning models in clinical settings. On a broader scale, Professor Bamba Gaye described efforts to scale telemedicine in Africa through crowdsourced data and collaborative strategies. For early-stage PhD students, it's crucial to develop an understanding of the value of clinical data and how to work with it thoughtfully and ethically.

Thanks to a generous contribution from the Software Sustainability Institute to my fellowship, we were able to host 20 PhD students from UCL and UCL-affiliated programmes overnight in Oxford. Combined with the fact that the conference was fully subsidised, this meant we could offer a high-quality, two-day event, including keynotes, poster sessions, and a formal dinner, at little to no cost to attendees. We were also delighted to award two poster prizes, recognising outstanding PhD research presented during the conference. 

The SSI’s support not only made this event more accessible but also helped foreground one of its most important themes: the responsible and thoughtful use of clinical data. From early-stage PhD students to experienced researchers, there was a shared recognition that technical progress must go together with ethical, context-aware data practices. We’re grateful for the opportunity to bring these conversations to the forefront and look forward to continuing this focus in future events.

Thanks to Software Sustainability Institute funding, I attended the first Town Hall meeting for the recently UKRI-funded Toward a new CCP for Arts, Humanities, and Culture research (CCP-AHC) project. CCP-AHC is principally focused on strengthening knowledge about large-scale compute (or high performance computing) and other advanced digital research infrastructures (DRI) for research software in the arts and humanities developed in the UK. The Town Hall focused on soliciting ideas, questions, and updates from scholars in these fields already engaging with DRI resources. I attended the meeting as the director of the MapReader software library, but also with my hat on as an SSI Fellow interested in the broader concerns around research software development and maintenance in the humanities. 

But what is a CCP and why are arts, humanities, and cultural heritage researchers moving towards this? “Collaborative Computational Projects” are funded by UKRI councils and administered by the Computational Science Centre for Research Communities (CoSeC) programme within UKRI’s Science and Technology Facilities Council. CCP-AHC was funded by a 2024 call designed to prepare new scholarly communities to apply for CCP funding in 2026. For the first time, potential future CCPs within the remit of AHRC and ESRC were eligible. As one of 6 new communities, the remit of CCP-AHC is above all to develop a roadmap and plan for the new CCP. In short, CCPs provide long-term funding for academic communities whose work depends on collectively used and maintained sustainable research software. For arts and humanities researchers to have access to such support would be a major stepping stone towards better national recognition of the computational needs of these disciplines.

Led by Eamonn Bell (Durham) with co-leads Karina Rodriguez-Echavarria (Brighton) and Jeyan Thiyagalingam (STFC), at the heart of the CCP-AHC is the issue of scaling up arts and humanities compute activities. As the UK invests in compute, it has been rare for humanities scholars to join the queues waiting to get access. When the MapReader team applied for access to the Bristol-based Isambard AI for some large-scale data processing tasks, we were welcomed with open arms as a novel use case in the humanities. Throughout 2024 and 2025, we used Isambard AI, Baskerville, the N8 Bede, and Lancaster’s HEC for a range of MapReader tasks. For example, for the “Landscape Change and Conservation with MapReader” project at Lancaster, Computational Environmental History Research Associate Kirsty Lilley created the UK’s first open-access datasets of historical vegetation and other landscape features from nineteenth-century Ordnance Survey maps in collaboration with the Peak District and South Downs National Parks (data paper forthcoming!). Simultaneously, we were also using Baskerville for large-scale text processing tasks with historical newspapers (for the now concluded Living with Machines and Data/Culture projects at The Alan Turing Institute). Indeed, because of her work with HPCs for the computational analysis of maps and newspapers, our Turing colleague Rosie Wood was honoured as one of the “Women in HPC” at SC2025 (SuperComputing: The International Conference for High Performance Computing, Networking, Storage, and Analysis).

For scholars to engage with big collections of historical sources that have now been scanned as images, and sometimes further digitised as structured or unstructured data, access to advanced computing resources is essential, and the CCP-AHC can address these needs in a coordinated fashion. With MapReader, and with the Living with Machines newspaper work, we learned two lessons the hard way: 

1. Assuming you will process data on your local machine puts strict limits on your dataset processing capacity, and for many colleagues without access to a powerful local computer, this is indeed out of the question. We knew we wouldn’t be using local compute for a lot of work, but it did create barriers within the team because core big data sets could be harder to access, sample, and explore from cloud storage locations.
2. Levelling up to using cloud-based virtual machines is extremely costly. For what we spent on commercial cloud-based compute and storage, we could have extended contracts or hired new team members. At the beginning of Living with Machines (ca. 2019), there was no alternative, and by the time we did have access to other, HPC infrastructure (e.g. Baskerville), we did not have time to rewrite code to work in a new environment or permission to move certain data.

I’m thrilled that colleagues across the UK might, through a new CCP, work together to avoid missed compute opportunities, develop HPC skills, and ensure HPC access. CCP-AHC has rightly identified knowledge about large-scale compute as a blocker to novel computational research in AHRC disciplines, but I would also highlight that this is not the only infrastructural challenge we face. From the lack of a robust, central data service for arts and humanities data to the importance of embracing and maintaining minimal computing workflows (in particular because these are more accessible to students and collaborators who do not have access to HPCs). But perhaps above all, there has been simply a dearth of opportunities to maintain humanities and arts research software as open-source projects. Older CCPs have used STFC support to ensure that key software can live on past its initial development funding. SSI’s Research Software Maintenance Fund offers one solution to this funding gap, but the long-term support of a CCP is unique in the UK. As it develops the roadmap for the future CCP, this is an exciting moment to see how the CCP-AHC leads and the broader community wish to shape computational research infrastructure for the arts and humanities going forward.

If the first Town Hall meeting opened up many perspectives on what we lack in terms of support for building capacity around DRI and sustaining software in the arts and humanities, future events will collect evidence from colleagues based on where they are at now. The CCP-AHC team is collecting information from UK colleagues about research projects using computational resources at all scales. If you’d like to learn more and potentially submit evidence about your own work, check out the details on the dedicated webpage.