This week, the BrainGlobe Initiative team received recognition from UCL Open Science for their contribution to open-source software. BrainGlobe was founded in 2020 to improve the way neuroscientists handle and analyse neuroimaging data, and its tools have since been downloaded over 2.7 million times. 

Visualising the brain

The BrainGlobe Initiative is an open-source, collaborative project that focuses on developing tools and software for the neuroscience community. Its main goal is to improve the way neuroscientists analyse and visualise neuroimaging data.

Brain mapping – the process of studying and visually representing the structure and function of the brain at various levels – increasingly involves huge and complex data sets. This includes large-scale anatomical structures derived from technologies like MRI scans, to detailed cellular activity data derived from 2-photon microscopy.

A key part of the initiative is to create software and platforms that work beyond a single imaging method or a single species, saving time, effort, and duplication.

Open Science

Alessandro Felder, technical lead for the BrainGlobe initiative and Senior Research Software Engineer at the Sainsbury Wellcome Centre (SWC) emphasised the importance of open-source software:

“Open-source software is vital in science as it fosters transparency, reproducibility, and collaboration. Researchers can verify results, build on existing tools, and freely share methods, accelerating scientific progress.”

“We are delighted to win this award and proud that BrainGlobe is serving the global neuroscience community working to understand the form and function of the brain.”

Open-source software also brings benefits in terms of scale, saving time as researchers can easily share data and tools. Alessandro additionally highlighted that open-source software is more robust and sustainable than closed-system software. With many people using and maintaining it, software can stay up-to-date, and the BrainGlobe team have recently been improving test code, implementing benchmarks and consistently testing across operating systems.

Cave fish and crabs

One of the latest collaborations for the BrainGlobe team is with researchers at the St. John’s University in the USA. Researchers there are studying the evolution of vision in cave fish species that have lost their sight, depending on how deep in the water they dwell. They are interested in what the ‘visual’ parts of the brain do when there are no eyes. Researchers at St. John’s University brought their cave fish brain atlas to the BrainGlobe team, to make it useable with the open-access tools. They worked together to incorporate the atlas, and the US researchers also helped with some of the software development. 

Closer to home, Alessandro and the team are building a brain atlas for the fiddler crab, which is being used at the SWC to study how animals navigate. They will draw on their experience creating an atlas de novo for a migratory bird species, and an ongoing collaboration on an atlas for the poison frog tadpole.

“The more species we work on, the better the tools become. There is increasingly an understanding that the model species, like mice or zebrafish, can only tell us so much in neuroscience. Including a diversity of species is hugely important if we are to understand the brain,” says Alessandro.

Current and future work

BrainGlobe was co-founded by Adam Tyson and Federico Claudi together with researchers at the Sainsbury Wellcome Centre and the Technical University of Munich. It is now a multi-national consortium of neuroscientists and developers. The team puts a lot of care into creating a consistent, intuitive graphical user interface for all the software. 

“We want to make the tools we have as accessible as possible and design them to be very easy to use. You don’t need to have programming experience to use BrainGlobe tools – that’s very important,” said Alessandro.

The team are also working on reducing bottlenecks in data processing, for example by speeding up the time it takes for microscope images to be reconstructed into a 3D image of the whole brain or creating a tool that allows images of parts of the brain to be aligned to the whole.

About BrainGlobe

•    BrainGlobe website https://brainglobe.info/
•    BrainGlobe software https://github.com/brainglobe