Advancing FAIR Neuroscience: Hands-On Learning with the EBRAINS Research Infrastructure

The neuroscience community continues to embrace openness and collaboration, and the recent INCF Workshop on FAIR Neuroscience provided researchers with an immersive opportunity to explore advanced tools and techniques for data sharing, analysis, visualization, and simulation.

Date: 25 - 26 August 2025
Location: Karolinska Institutet, Stockholm, Sweden
Organized by: INCF in collaboration with SeRC and EBRAINS

Hosted in collaboration with the Swedish e-Science Research Centre (SeRC) and EBRAINS Research Infrastructure, the event brought together neuroscientists, data scientists, and students from diverse backgrounds to learn how to manage, share, and analyze data using EBRAINS tools and services. Through a series of guided sessions and hands-on tutorials, participants gained practical experience in applying FAIR (Findable, Accessible, Interoperable, and Reusable) data principles in neuroscience.

The workshop also featured an introductory Python programming session for neuroscientists, designed to support beginners interested in developing computational and data analysis skills.

Workshop Sessions

The event began with a series of presentations introducing the principles and practices of FAIR neuroscience and the capabilities of the EBRAINS ecosystem:

• Introduction to FAIR Neuroscience
  Led by Mathew Abrams (INCF Secretariat), participants explored the FAIR principles and discussed how these guidelines enhance reproducibility and data sharing in neuroscience.
   
• The EBRAINS Ecosystem for Sharing, Finding, and Using Neuroscience Data
  Led by Trygve Leergaard (University of Oslo), this session guided attendees through the EBRAINS platform, highlighting its integrated tools for collaboration and open data discovery.
   
• EBRAINS Data and Knowledge Services: Impactful Data Sharing
  Led by Sophia Pieschnik, Signý Benediktsdóttir, Maya Kobchenko, Archana Golla (University of Oslo), Attendees learned practical approaches to making neuroscience data discoverable and reusable through EBRAINS infrastructure.
   
• Consultation Sessions (EBRAINS Data Curation Team)
  Researchers had the opportunity to discuss their own data-sharing challenges and receive personalized guidance from EBRAINS and INCF experts.

Hands-On Tutorials

The QUINT Workflow: Whole-Brain Section Mapping Using Atlases and Machine Learning (Maja Puchades, University of Oslo)

Led by Maja Puchades (University of Oslo), participants explored the QUINT workflow, a user-friendly analysis solution for 2D rodent brain microscopy data. The workflow allows for brain-wide mapping and regional quantification using reference atlases—no coding required. Attendees practiced generating labeled object counts, area fractions, and 3D visualizations aligned to atlas spaces.

Navigating and Visualizing Brain Data with EBRAINS Atlas Resources

Led by Maja Puchades and Trygve Leergaard (University of Oslo), this tutorial demonstrated how to use EBRAINS’ open-access 3D brain atlases for navigating neuroanatomy, defining regions of interest, and creating high-quality visualizations. Participants brought their laptops for hands-on exploration and practical examples of applying these tools in their own research.

Using EBRAINS Atlas Services with Siibra and Voluba

Led by Sebastian Bludau and Ahmet Nihat Simsek (Research Centre Jülich), this session introduced participants to three key tools — siibra-explorer, siibra-python, and Voluba — for multilevel brain atlas exploration. Attendees learned to:

• Access and visualize 3D reference templates and parcellation maps
• Explore multimodal regional data from the BigBrain dataset
• Use siibra-python for extracting cortical and connectivity features
   

The tutorial bridged visual interfaces with computational workflows, supporting both beginners and experienced users.

Managing and Analyzing Electrophysiology Data with Neo and Elephant

Led by Michael Denker and Julio Rodino (Research Centre Jülich), participants gained experience with Neo and Elephant, Python-based tools for representing and analyzing electrophysiology data such as spike trains and local field potentials. The tutorial covered data handling, analysis workflows, and metadata integration for reproducibility using EBRAINS e-infrastructure services.
 Basic Python knowledge was recommended.

From Single-Cell Models to Large-Scale Network Dynamics with NEST Simulator

The final tutorial featured NEST, an open-source simulator for spiking neuronal networks, led by Sebastian Spreizer (University of Trier). Starting with the intuitive NEST Desktop interface, participants built and analyzed neuron models before progressing to Python-based simulations in Jupyter notebooks. The session concluded with an introduction to NESTML, where attendees designed custom neuron and synapse models to simulate biologically realistic network dynamics.

Toward a More Open and Reproducible Neuroscience

By combining conceptual presentations, interactive tutorials, and open discussions, the INCF–SeRC–EBRAINS workshop offered a comprehensive introduction to the EBRAINS Research Infrastructure and the FAIR data principles driving modern neuroscience.

Participants left with new skills, deeper understanding of open science practices, and practical experience using powerful tools to analyze and visualize brain data. The event also fostered meaningful connections among researchers, strengthening the growing global community committed to open, FAIR, and collaborative neuroscience.

Acknowledgements

This workshop was organized by the International Neuroinformatics Coordinating Facility (INCF) in collaboration with Swedish e-Science Research Centre (SeRC) and EBRAINS. We extend our gratitude to all instructors, speakers, and participants for their engagement and contributions.

For more information about upcoming training opportunities and workshops, visit INCF Training Space or EBRAINS Training, or contact training@incf.org.