5th Workshop on Neuroengineering: AI tools in Neuroscience

27-28 October 2025 | i3S – Instituto de Investigação e Inovação em Saúde

In recent years, artificial intelligence (AI) has taken the world by storm, rapidly transforming a wide range of fields - from industry and healthcare to education and research. Inspired by fundamental principles of brain function, AI is now reshaping how scientists study the brain itself. In this workshop, we will explore the latest breakthroughs at the intersection of AI and neuroscience, highlighting how machine learning and data-driven approaches are revolutionizing neuroengineering and our understanding of neural systems.

By integrating hands-on practical sessions, the workshop also gives the possibility for the interested participants to try basic techniques used in neuroengineering, as well as neuroscience-relevant AI tools.

This 5th edition of the WoN includes 3 selected short-talks from students and junior researchers, as well as a poster session. We thus invite the participants to submit their recent work.

Organizers: Paulo Aguiar, Miguel Aroso, José Mateus

Target audience: Researchers and students (MSc and PhD) working in neuroscience/neurobiology, biomedical engineering, biophysics, and related fields. The hands-on practical sessions are targeted for students (MSc and PhD) but are open to everyone. Every practical session has a duration of 3h and each participant can only register in one hands-on practical session.

Poster >>

The workshop will be held at i3S – Instituto de Investigação e Inovação em Saúde.
Rua Alfredo Allen, 208; 4200-135 Porto, Portugal
Tel: +351 226 074 900 | Site: http://www.i3s.up.pt/ | E-mail: events@i3s.up.pt
GPS coordinates: 41º 10’ 30.008’’ N, 8º 36’ 12.488’’ W.

First day | 27th October 2025: Seminars.
Second day | 28th October 2025: Hands-on practical sessions on basic lab techniques in neuroengineering and AI tools.

Schedule

First day | 27th October 2025

09:15 - 09:35 Welcome Coffee

09:35 - 09:45 Introduction

09:45 - 10:30 Engineering neurohybrid interfaces
Francesca Santoro, RWTH Aachen and Forschungszentrum Juelich, Aachen, Germany

10:30-11:15 Dynamics and effective connectivity in neuronal cultures with topographical substrate.
Jordi Soriano, Institute of Complex Systems, University of Barcelona, Barcelona, Spain

11:15 - 12:00 Reservoir computing with biological neural networks: A bottom-up approach to neural computation
Hideaki Yamamoto, Tohoku University, Sendai, Japan

12:00 - 13:30 Lunch

13:30 - 14:15 Nonlinear state space modeling of neural time series
Memming Park, Champalimaud Research, Lisbon, Portugal

14:15-15:00 Data science and neuroengineering approaches enable neurorehabilitation
Miguel Castelo-Branco, CIBIT, Coimbra, Portugal

15:00 - 15:10 Sponsor Talk
MaxWell Biosystems

15:10 - 16:00 Selected Orals 

Transcription Factor-Mediated Glial Reprogramming as a Therapeutic Strategy for Machado-Joseph Disease
Catarina Miranda, Center for Neuroscience and Cell Biology, University of Coimbra (CNC-UC)

Biomimetic signal generators in epilepsy neuromodulation with reservoir computing
Adam Armada-Moreira, University of Modena and Reggio Emilia

From Simulation to Experiment: Reinforcement Learning for Real-Time Closed Loop Neuromodulation
Eduardo Fernandes de Carvalho, i3S

16:00 - 16:45 Coffee Break & Poster session

16:45 - 17:30 Using machine learning to classify neuronal activity encoding rewarding and aversive stimuli
Ana João Rodrigues, ICVS/School of Medicine, University of Minho, Braga, Portugal

17:30 Concluding Remarks

Second day | 28th October 2025

09:30-12:30 Hands-on practical morning session

14:00-17:00 Hands-on practical afternoon session

Hands-on Practical Sessions
Please note that the number of available seats in some sessions is very low.
The minimum number of participants per session is 2.

S1 – Basics of Neuronal Cell Cultures 
This session is intended to provide introductory training in the basic requirements for successful cell culturing. Through this hands-on training session, participants will become familiar with various valuable resources and guidelines necessary for maintaining a cell culture of induced pluripotent stem cells (iPSCs).
[Responsible: Ricardo Pinto, NCN/i3S].

S2 - Preparation of brain-on-a-chip platforms 
Brain-on-a-chip platforms have been increasingly used in neuroscience, as they allow to mimic neural circuits through spatial and/or fluidic compartmentalization of cells, as well as to model several neuropathological scenarios. During this session, participants will be introduced to brain-on-a-chip platforms and will be able to prepare their own microfluidic devices.
[Responsible: Sara Silva, NCN/i3S]

S3 – Introduction to NEURON – in silico neuroscience and detailed simulations of neurons in a computer 
This session gives an introduction to the NEURON simulation environment, a well-established tool for in silico neuroscience. Participants will learn how to perform biophysically detailed simulations of single neurons and small neuronal circuits. Participants are requested to bring their laptops for this session.
[Responsible: Paulo Aguiar, NCN/i3S].

S4 – Principles of microelectrode arrays (MEA) electrophysiology 
Microelectrode array (MEA) technology enables electrophysiological recording and/or stimulation of hundreds of neurons simultaneously. In this session, the participants will get acquainted with the principles of MEA experiments and have the possibility to evoke and record extracellular signals from neuronal networks.
[Responsible: José Mateus, NCN/i3S].

S5 – Imaging neuronal activity with Calcium dyes 
Calcium dyes are used to monitor neuronal activity by assessing the resulting intracellular changes in Ca2+ concentration. In this session, participants will have the opportunity to image neuronal cell cultures labeled with a calcium dye and analyze the acquired data with software developed in-house.
[Responsible: Miguel Aroso, NCN/i3S].

S6 – AI in Magnetic Resonance Imaging (MRI) 
MRI is a non-invasive technique comprising various imaging modalities, widely applied in clinical practice and biomedical research. AI-assisted processing and data analysis will be explored, featuring hands-on examples spanning anatomical, microstructural, and metabolic neuroimaging.
[Responsible: Rui Simões, NCN/i3S]

S7 – Gen-AI in neuroscience 
Large Language Models (LLMs) offer powerful capabilities for enhancing various stages of the scientific research process. In this session, participants will become familiar with the practical application of LLMs in health research, with a focus on prompt engineering, automated literature summarization, and hypothesis generation. Through guided exercises and interactive demonstrations, they will have the opportunity to explore key tools and platforms that facilitate the integration of LLMs into real-world research workflows.
[Responsible: Sara Sousa, NCN/i3S]

S8 – Building and training an artificial neural network (ANN) with python 
In this workshop, participants will learn how to construct and train an artificial neural network (ANN) using Python - an algorithm inspired by the brain’s neurons but translated into code. Through intuitive analogies, we’ll demystify key concepts like weights, activation functions, and backpropagation. Participants will build a simple ANN from scratch and practice training and evaluating models on real-world data. No advanced math background is needed - just bring curiosity and enthusiasm for bridging biology and machine learning!
[Responsible: Eduardo Carvalho, NCN/i3S]

Francesca Santoro
RWTH Aachen and Forschungszentrum Juelich, Aachen, Germany

Francesca Santoro, born in Naples in 1986, is a biomedical engineer specialed in neuroelectronics. She earned her Bachelor's and Master's degrees in Biomedical Engineering at the University of Naples Federico II, followed by a PhD from RWTH Aachen and Forschungszentrum Juelich in 2014. After a postdoctoral fellowship at Stanford University, she founded the Tissue Electronics Lab at the Istituto Italiano di Tecnologia. Currently, she is Full Professor and Head of the Neuroelectronic Interfaces Lab at RWTH Aachen and Forschungszentrum Juelich. Her awards include the MIT Technology Review Under 35 Europe and Italy, an ERC Starting Grant, the Falling Walls Breakthrough Award, and early career recognition from the German National Academy of Sciences Leopoldina. She has published over 80 peer-reviewed articles and delivered more than 60 talks at major international conferences.

Jordi Soriano
Institute of Complex Systems, University of Barcelona, Barcelona, Spain
Jordi Soriano holds a bachelor’s in physics from the University of Barcelona combined with a PhD in condensed matter physics (University of Barcelona, 2003). He carried out postdoctoral stays at the University of Bayreuth (Germany) and the Weizmann Institute of Science (Israel), exploring problems in biophysics and neuroscience from a complex systems perspective. In 2008, Jordi established his own group and laboratory in neuroscience at the University of Barcelona, with the aim to investigate neuronal cultures as a model system for both physics and medicine, and combining state-of-the-art experimental tools with resources from network theory and dynamical systems.

Hideaki Yamamoto
Tohoku University, Sendai, Japan
Hideaki Yamamoto received his Ph.D. degree in Engineering from Waseda University in 2009. After working as a JSPS Research Fellow at Tokyo University of Agriculture and Technology and as an Assistant Professor at Waseda University, he joined Tohoku University in 2014 as an Assistant Professor at the Frontier Research Institute for Interdisciplinary Sciences. Since 2020, he is an Associate Professor at the Research Institute of Electrical Communication, Tohoku University. His major interest is in exploring novel applications of engineering technologies to gain constructive understanding of biological systems.

Ana João Rodrigues
ICVS/School of Medicine, University of Minho, Braga, Portugal

Ana João Rodrigues is a Group Leader at ICVS and Invited Professor at the School of Medicine, University of Minho. Her research bridges fundamental and clinical neuroscience, integrating rodent and human studies to elucidate the neural mechanisms underlying motivated behaviors. Her laboratory employs a multidisciplinary approach, combining behavioral assessments, optogenetics, electrophysiology, pharmacology, and live imaging with genetically-encoded sensors in rodent models to understand how reward and aversion are encoded in the brain. Beyond research, she is deeply committed to science communication and public engagement, having led multiple initiatives over several years to promote scientific literacy in the general public.

Miguel Castelo-Branco
CIBIT, Coimbra, Portugal

Miguel Castelo-Branco (MD PhD), is Full Professor at the University of Coimbra, is the Scientific Coordinator of the National Brain Imaging Network,   Director of CIBIT, and Vice-Director of ICNAS, the Medical Imaging Infrastructure at the University of Coimbra, working in the fields of NeuroEngineering and Cognitive/Clinical Neuroscience. He obtained his PhD at the Max-Planck Institute for Brain Research, Frankfurt, Germany. He has held a Professorship in Psychology at the University of Maastricht, the Netherlands, where he is now Affiliate Professor. Before, he was also a Postdoctoral fellow at the Max-Planck-Institute for Brain Research, Germany.

Memming Park
Champalimaud Research, Lisbon, Portugal

Memming Park is a Group Leader of the Neural Dynamics Lab and Co-Director of the Neuroscience PhD Program at the Champalimaud Centre for the Unknown. Previously, he was an Associate Professor of Neurobiology and Behavior at Stony Brook University. Memming received his BS in Computer Science from KAIST, MS in Electrical Engineering and PhD in Biomedical Engineering from the University of Florida, and completed his postdoctoral training with Jonathan Pillow. He has been recognized with the NSF CAREER Award and the Discovery Prize. With his background in neural signal processing and machine learning, Memming focuses on data-driven modeling of meaningful behavior and the development of innovative neural data analysis methodologies.
https://catniplab.github.io/

This 5^th edition of the WoN will include 3 selected short-talks from students and junior researchers, as well as a poster session. We thus invite the participants to submit their recent work. Up to five abstracts submitted by SPN members will be selected to receive a waiver that covers the workshop registration fee. The abstract submission deadline is 12^th September, with notifications sent by 15^th September.

Your submitted Abstract should be 1 page PDF with no more than 500 words, but may include figures.

Abstract submission deadline: 12^th September (notification of results on 15^th September)

Abstract submission form >>

A participant can register for the lectures only (27^th October 2025), for a hands-on session only (28^th October 2025), or for both lectures and one hands-on session. The registration fees include the coffee break and lunch (27^th October 2025 only) and the necessary hands-on session materials.

Please notice that the number of seats is limited (for both lectures and practical sessions).
Participation will be confirmed on a first-come, first-served basis, upon confirmation of registration fee payment.
The time slot (morning or afternoon) for each practical session is subject to confirmation.
This information will be provided to the participants upon registration.

Registration fees:

Registration form >>

More information:
Events Management Unit | Rua Alfredo Allen 208 | 4200-135 Porto, Portugal
Email: events@i3s.up.pt | Tel: +351 226 074 900