EBRAINS users days - Agenda

We recommend to attend "in person" in Heidelberg. For people, who can not make it: The talks during the introduction day (6 October) will also be streamed (free of charge) via zoom. Please register here for attending via zoom online stream.

Venue: at the EINC in Heidelberg, Germany

Street address: Im Neuenheimer Feld 225a, 69120 Heidelberg, Germany.
Please see the EINC page for tram and parking info.

Registration

The registration fee of 25 Euro / day includes the lunch at Heidelberg University mensa, coffee breaks and cookies.
To register for the users day:

• if you have an EBRAINS account (recommended) please register here with EBRAINS account
• else (i.e. if you do not (yet) have an EBRAINS account), please register here

(To request a free-of-charge EBRAINS users account please use https://ebrains.eu/register)

The registration deadline for on-site-attendance is Thursday, 1 October 2026
Until the meeting on 6 October you can still register for attending via zoom online stream -- see above for the URL

Posters

12 poster boards in the coffee break area are available (contact Björn to reserve one) to highlight tools or services and serve as conversation-starters:

• The EBRAINS Software Distribution (ESD)
• BrainScaleS neuromorphic compute system
• EBRAINS tools-for-teaching
• Clinical Connectome
• 5M Connectome
• In-depth metadata in the KG - enabling data reuse

(for linking to the agenda this ebrains.eu URL can be used.) .

Collect your name-tag and a cookie.

• Jan Bjaalie: An introduction tour through the whole EBRAINS Research Infrastructure
• Boris Orth: The cloud, storage and HPC infrastructure powering EBRAINS

Introduction + panel discussion with audience feedback

Panelists :

• Andrew Davison
• Eszter Papp
• Amaryllis Raouzaiou
• Oliver Schmid

Instruct-ERIC is a pan-European distributed research infrastructure making high-end technologies and methods in structural biology available to users. In July, EBRAINS and Instruct-ERIC signed a Memorandum of Understanding, establishing a strategic collaboration to strengthen links between digital neuroscience and structural biology research infrastructures in Europe.

An introduction to the core platform services of the EBRAINS research infrastructure, highlighting its shared workspaces, storage solutions, and interactive computing environments.

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An introduction on how to prepare for curation of datasets, models or software for inclusion in the EBRAINS RI knowledge graph and data sharing services

Introduction of the ways the EBRAINS team can help creating a sound proposal for applying for High Performance Compute (HPC) resources for research cases, where local compute power is insufficient.

The EBRAINS software distribution provides a software environment (container) for using lots of EBRAINS tools in the same setup - from usage on an individual system up to HPC environments. This session demonstrates the process (download, use, scale up).

Workflows combining different tools potentially running at different sites (e.g. for accessing local data sets and leverage compute power).

• Platforms overview
• Introduction to the PHI-Platform for Human Imaging

Workflows introductions to the cerebellar models repo and the Cerebellar-hub

There slots, 2h each, of parallel offers for hands-on tutorials.

For most of the EBRAINS tools used in the tutorials an EBRAINS account will be needed. Best get your account ahead of time. If that is not possible you can also get a guest account on the spot to be able to participate in the hands-on tool usage sessions.

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Siibra-python in action

Advanced workflows with siibra-python - Bring your own data (by Dr. Ahmet Nihat Simsek & Dr. Xiaoyun Gui)

The siibra toolsuite provides programmatic access to the EBRAINS multilevel brain atlas, integrating reference spaces, parcellation maps, and a broad range of multimodal neuroscience data. In this advanced, hands-on tutorial, participants will learn how to use siibra-python to integrate and analyse their own data in an atlas context. Following a Bring Your Own Data approach, participants are encouraged to work with NIfTI images, such as fMRI activation maps, or sets of spatial coordinates. Example datasets will be provided for participants who do not bring their own data. The tutorial will cover advanced workflows for anatomical assignment and spatial analysis, including the probabilistic assignment of participant data to cytoarchitectonic brain regions and its integration with multimodal information available through EBRAINS, such as receptor densities, connectivity, cellular and microstructural data, and high-resolution BigBrain data. Participants will learn how to use siibra-python to place their own data into an anatomical context and combine it with multimodal information from the EBRAINS multilevel brain atlas.

Recommended preparation: Basic experience with Python/Jupyter is recommended. Participants wishing to bring their own data should provide NIfTI images or spatial coordinates in MNI152/ICBM152 space.

Integrated visual simulation and analysis workflows using NEST Desktop and Elephant Lab

In this introductory level tutorial we will introduce participants to analyzing electrophysiological data from simulation and experiment using the tools

• Neo (https://neuralensemble.org/neo) for representing and handling the data, and
• Elephant (https://python-elephant.org) for performing the actual analysis.

We will cover using the basic data objects, loading realistic datasets and performing analysis protocols using a novel intuitive interface (Elephant Lab). In addition, we will demonstrate how to prototype a spiking neuronal network simulation using the NEST Desktop graphical tool, transfer the simulation to the EBRAINS Jupyter environment, and analyze the simulation output in Elephant Lab. For the tutorial, participants will be able to follow the tutorial using the EBRAINS Collaboratory.

EBRAINS demonstrators: Sensorimotor neurocontroller and Epileptic virtual brains

• The " sensorimotor neurocontroller" workflow will show how spiking neural networks interact with embodied physics, and how cerebellar plasticity models can be tested in closed-loop conditions, with planner, motor cortex and sensory feedback. We will show this sensorimotor control system in multiple trials of reaching, exploring multiple target object positions and multiple perturbation forces, to define quantitative relationships with the performance accuracy along trials. Please find more details and an architecture description of the Sensorimotor neurocontroller here
• The " Epileptic virtual brains" workflow will show how stimulation impacts in epilepsy, by interfacing the epileptogenic zone network with electrode field calculations,in high-resolution whole-brain simulation (TVB)

5M Connectome Tutorial

The tutorial starts with a brief recap of the feature download process covered in the PHI tutorial, together with a walkthrough of the feature data directory structure, what is available and how it is organized. Participants then download, via the notebook, a subsample of 5M features. This is followed by a demonstration of a typical harmonization workflow using ComBat, to correct for site and scanner effects across the multicentric dataset. Finally, a worked example shows multimodal integration, combining features from different modalities (EEG, MRI, PET) around a sample scientific question, to illustrate how harmonized multimodal data can be used in an actual analysis.

The parallel tutorials

More information about the tutorials in this slot:

show abstract

Infos:

• On the day after the EBRAINS users days the education department of the EBRAINS 2.0 project organizes a students day Please find the agenda of the students day (8 October 2026). here
• If you want to experience another hands-on tutorial (only online, though): The "Virtual users days" happen from 12-14 October 2026