All posts by Catarina

Frontiers in Neural Organoids Modelling

Course overview

The course provides advanced training into the field of neural organoids for the modeling of brain development and physiopathology. Neural organoids, three-dimensional models derived from human pluripotent stem cells, have been revolutionizing the study of the human brain and its disorders by recapitulating key steps of human brain development including neural stem cells patterning, expansion, differentiation and connectivity. Moving beyond a basic introduction, this intensive course will focus on emerging frontiers research directions, equipping the next generation of neuroscientists with cutting-edge frontier know-how.

The course emphasizes an integrative, hands-on approach that bridges the gap between theoretical knowledge and practical applications by combining experimental and computational methods. Participants will gain a sophisticated theoretical framework and the practical insights to pursue the frontiers of neural organoid modelling in their own research.

Course directors

University of Milan and Human Technopole, Italy

Yale University, USA

Scientific Directors

University of Milan and Human Technopole, Italy

Yale University, USA

Human Technopole, Italy

Keynote Speakers

Will be announced soon!

Instructors

Will be announced soon!

Course content

Topics

This course will focus on five themes:

● Neural organoids for population-scale neurodevelopmental modelling to connect molecular and clinical phenotypes;

● Mosaic models to understand the molecular basis of clonal dynamics and non-cellautonomous effects in the human brain;

● Mathematical modelling of neural organoid biology;

● Morphogen patterning as a driver of brain region and cell lineage specification and a source of biases in brain morphogenesis;

● Somatic mutations in pluripotent lines to trace developmental lineages.

Aims and Techniques

The primary objective of this intensive course is to equip young neuroscientists with the sophisticated theoretical framework and practical expertise required to successfully implement neural organoids in their own research endeavors.

Upon completion of the course, participants will be able to:

● Demonstrate a comprehensive understanding of the principles of differentiation of

pluripotent stem cells into different neural organoid types.

● Critically assess the advantages and disadvantages of neural organoid modelling and select the most appropriate designs for their research questions.

● Master essential techniques for the characterization of neural organoids, including multiplexing approaches to scale-up modelling, integrating molecular and clinical endophenotypic scales, and dissecting unexplored dynamics of developmental systems.

● Design and execute experiments leveraging neural organoids to model complex physiopathological processes, through a combination of experimental and computational approaches.

● Establish a professional network with leading scientists and peers, fostering future collaborations and career development.

Bordeaux School of Neuroscience, France

The Bordeaux School of Neuroscience is part of Bordeaux Neurocampus, the Neuroscience Department of the University of Bordeaux. Christophe Mulle, its current director, founded it in 2015. Throughout the year, renowned scientists, promising young researchers and many students from any geographical horizon come to the School.
The school works on this principle: training in neuroscience research through experimental practice, within the framework of a real research laboratory.

Facilities
Their dedicated laboratory (500m2), available for about 20 trainees, is equipped with a wet lab, an in vitro and in vivo electrophysiology room, IT facilities, a standard cellular imaging room, an animal facility equipped for behavior studies and surgery and catering/meeting spaces. They also have access to high-level core facilities within the University of Bordeaux. They offer their services to international training teams who wish to organize courses in all fields of neuroscience thanks to a dedicated staff for the full logistics (travels, accommodation, on-site catering, social events) and administration and 2 scientific managers in support of the experimentation.

Registration

Fee : 5.000 € (includes tuition fee, accommodation and meals)

Applications will open soon.

Quantitative Approaches to Behaviour and Virtual Reality

Course overview

Quantitative studies of behaviour are fundamental in our effort to understand brain function and malfunction. Recently, the techniques for studying behaviour, along with those for monitoring and manipulating neural activity, have progressed rapidly. Therefore, we are organizing a summer course to provide promising young scientists with a comprehensive introduction to state-of-the-art techniques in quantitative behavioural methods. This course’s content is complementary to other summer courses that focus on measuring and manipulation neurophysiological processes.

Our focus is on methodologies to acquire rich representations of behavioral data, dissect them statistically, model their dynamics, and integrate them with other kinds of neurobiological data to address scientific questions. To this end, students will 1) fabricate devices for recording the behavior experimental organisms, 2) learn, under the guidance of the scientists developing these methods, the modern tools to analyze behavioral data from these organisms, and 3) in a week-long independent project develop and conduct a behavioral study of their own design, with the support and guidance of the course instructors and teaching assistants.

The course content is designed to be translational. Methodologies and analytical frameworks developed for one model organism can be adapted and applied across species, from invertebrates to humans. Understanding the behavioral repertoires and experimental possibilities in both simple model systems like flies and complex organisms like humans will significantly expand students’ experimental horizons and research capabilities.

Course directors

Northwestern University, USA

Imperial College London, UK

Champalimaud Research, Portugal

Keynote speakers

Will be announced soon!

Instructors

Will be announced soon!

Course content

This 3-week course is a practical “hands-on” introduction to advanced methods in behavioural tracking and analysis. Our educational goal is to cover sufficient background such that all participants will be able to establish these techniques in their home laboratories.

In the pedagogical portion of the course (blocks 1 and 2) we will use three main experimental model systems: flies (Drosophila melanogaster), fish (Danio rerio), and humans (Homo sapiens). Several days of instruction will focus on the analysis of video recordings of flies, fish, and humans as well as physiological signals and auditory recordings (from humans). On these days, students will perform analyses either on the data they acquired, on videos we provide of fish and rodents behaving, or on data from their own organism of choice.

In the student project portion of the course (block 3), students may develop their experiments using any of the three experimental model organisms from the course, or using other organisms in use at the Champalimaud (subject to their availability)
We will cover data acquisition (software, hardware, tools), data extraction (single animal, body part, and multiple animal tracking systems), data analysis (clustering, ethograms), and hypothesis-driven modeling (reinforcement learning, optimal feedback control).

Course format

TThe course is organized in three blocks. During the first block, the students will use flies, fish, and human participants to learn, through hands-on device fabrication, environment design, and data acquisition, how modern ethological methods like markerless tracking, virtual reality, automation, and optogenetics can be used for quantitative behavioral experiments.

In the second block, students will study data from a broader range of species while learning to apply quantitative analysis methods (e.g. unsupervised and supervised ethograms, manifold inference, deep neural networks, theoretical modeling) to tackle questions about behavior and brain function.

In the third block, students will form small groups and deploy these new skills to design and implement a week-long research project of their choice that consolidates this new knowledge, culminating in presentations of their findings. The extended project will offer an opportunity for the participants to undertake novel state-of-the-art research supervised by international experts in the field.

In addition:

– International speakers will give daily seminars to describe how quantitative tools of behavioural analysis have impacted their work. Several of these speakers will also conduct pedagogical sessions to instruct students in the devices and analyses they have developed. Students will have structured opportunities to interact scientifically and socially with course speakers outside of the lab.

– Students will give daily micro-presentations on their successes and failures implementing the instructed techniques of blocks 1 and 2.

– Students will give presentations, throughout the course, on the research they are pursuing in their home labs.

– At the end of block 3, students will present their independent projects in a culminating research symposium.

Champalimaud Centre for the Unknown, Portugal

The Champalimaud Foundation is a private, non-profit organization, established in 2005 and dedicated to research excellence in biomedical science. Completed in 2010, the Champalimaud Centre for the Unknown is a state-of-the-art centre that houses the Champalimaud Clinical Centre and the Champalimaud Research, with its three parallel programs – the Champalimaud Neuroscience Programme, the Physiology and Cancer Programme, and the Experimental Clinical Research Programme.
Initially focused on a system and circuit approach to brain function and behavior, the Centre expanded to incorporate molecular and cell biological expertise. The Centre comprises 26 research groups (circa 400 researchers) leading independent curiosity-based research.

Facilities
The Centre provides Facilities dedicated for Training, some in their entirety, for use by the CAJAL Advanced Neuroscience Training Programme. These include the Teaching Laboratory, a fully equipped open lab space for 20-30 students that can be dynamically reconfigured to support a full range of neuroscience courses. It also overlooks, via floor to ceiling windows, a tropical garden and the river. The experimental spaces include: Imaging Lab: A dark-room containing a full size optical table is used for advanced imaging setups (two-photon microscopy, SPIM, etc.) and custom (course-designed) optical systems.

Registration

Fee : 5 000 € (includes tuition fee, accommodation and meals)

Applications will open soon.

Neuromics – Single-Cell and Spatial omics in the Nervous System

Course overview

The field of neuroscience is undergoing a revolutionary transformation through the integration of cutting-edge genomic technologies with traditional neurobiological approaches. Single-cell and spatial genomics are unveiling unprecedented molecular insights into nervous system development, function, and disease, fundamentally changing our understanding of neural circuits and brain organization.

This intensive three-week course provides comprehensive hands-on training in state-of-the-art “neuromics” technologies, combining theoretical foundations with practical experience in single-cell genomics, spatial transcriptomics, and multi-omics approaches specifically applied to the nervous system. Participants will gain expertise in experimental design, data generation, computational analysis, and biological interpretation of high-throughput genomic datasets from neural tissues.

The course integrates lectures from world-leading scientists with intensive laboratory work, enabling participants to master both experimental protocols and computational pipelines essential for modern neuroscience research. Through collaborative projects, students will explore applications ranging from neural development and cell type identification to disease mechanisms and therapeutic targets.

Course directors

Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland

Department of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, Haifa, Israel

Interdisciplinary Institute for Neuroscience (IINS), CNRS, Université de Bordeaux, France

Keynote Speakers

Will be announced soon!

Instructors

Will be announced soon!

Target Audience: This course is designed for graduate students and postdoctoral fellows from diverse backgrounds including neuroscience, computational biology, and related fields. Participants should have basic knowledge of molecular biology and basic familiarity with programming for computational components. The course welcomes researchers from both experimental and computational backgrounds seeking to integrate new omics approaches into their neurobiology research.

Course Content and Techniques

Experimental Approaches

• Single-cell and single-nucleus RNA sequencing

• Spatial transcriptomics

• Single-cell epigenomics

• Multi-omics integration

• Sample preparation techniques for nervous system tissues

• Quality control and experimental optimization

Computational Analysis

• Single-cell data preprocessing and quality control

• Cell type identification and characterization

• Trajectory analysis and pseudotime reconstruction

• Spatial data analysis and tissue organization mapping

• Multi-omics data integration strategies

• Machine learning applications in single-cell genomics

• Visualization and interpretation of high-dimensional datasets

Applications in Neuroscience

• Neural development and differentiation trajectories

• Adult brain cell type taxonomy and function

• Disease mechanisms and biomarker discovery

• Comparative neuroscience across species

• Stem cell-based neural models and organoids

• Therapeutic target identification

Learning Objectives

Upon completion of this course, participants will be able to:

• Design and execute single-cell and spatial genomics experiments for neural tissues

• Apply appropriate computational methods for analyzing complex genomic datasets

• Integrate multi-modal data to address biological questions in neuroscience

• Critically evaluate and interpret results from high-throughput genomic studies

• Implement best practices for data management, reproducibility, and sharing

• Translate genomic findings into testable hypotheses for further research

Course Structure

The course combines keynote lectures from renowned experts in neuromics, hands-on laboratory sessions using cutting-edge technologies, computational workshops with real datasets, and collaborative group projects. Participants will work in small teams on mini-projects that integrate experimental and computational components, culminating in presentations of their findings. Journal clubs and expert panels will provide opportunities for scientific discussion and career development.

This comprehensive training program equips the next generation of neuroscientists with essential skills for leveraging genomic technologies to advance our understanding of the nervous system in health and disease.

Bordeaux School of Neuroscience, France

Registration

Fee : 5 000 € (includes tuition fee, accommodation and meals)

Applications will open soon.

The Neurovascular Unit and Beyond – How CNS Border Sites Dynamically Regulate Brain Homeostasis

Course overview

We are excited to announce a new 2026 Cajal Course to be focused on the CNS Borders and Barriers: ‘The Neurovascular Unit and Beyond – How CNS Border Sites Dynamically Regulate Brain Homeostasis.’ This topic could not be more topical at the present moment. Recent years have literally seen an explosion of foundational work on the CNS barrier / interface / border sites (Badaut et al. FBCNS, 2024). Today, we have an increasingly complex and nuanced understanding of the transcriptomics, anatomy, and functional correlates of these different interfaces. This knowledge has fueled a dramatic increase in translational applications (e.g. delivery approaches for biotherapeutics and small molecules) as well as an ongoing vigorous discussion about several aspects of the CNS border sites within the field.

We are now on the cusp of several new therapeutic approaches being fully translated into the clinic (e.g. Alison Abbott: Breaking down barriers in brain-drug research. Nature, 29 May 2025), in part due to a more complete understanding of neurovascular unit, choroid plexus, and leptomeningeal biology. Better appreciation of the physiology of brain fluids (cerebrospinal fluid, interstitial fluid) has also been informing much more sophisticated interpretation of biomarkers (e.g. neurofilament light chain) that increasingly underlie the monitoring of disease progression and responses to therapy. Finally, the large body of recent clinical (and pre-clinical) therapeutic CNS-directed work is in turn facilitating a more sophisticated reconsideration of the CNS border sites, allowing us to better comprehend critical physiological processes, species differences, and even evolutionary aspects related to brain homeostasis. It is an incredibly exciting time for the field! This course will explore these scientific areas with world class keynote lectures and laboratory modules led by a number of dynamic instructors at the forefront of the field.

Course directors

Centre National de la Recherche Scientifique (CNRS), France

Denali Therapeutics, South San Francisco, California, USA
University of Minnesota-Twin Cities, USA
Past President, International Brain Barriers Society

Keynote Speakers

Will be announced soon!

Instructors

Will be announced soon!

Course content

Projects

Will be announced soon!

Bordeaux School of Neuroscience, France

Registration

Fee : 5 000 € (includes tuition fee, accommodation and meals)

Applications will open soon.

Neurobiology of Sleep

Course overview

This inaugural Cajal Course on Neurobiology of Sleep offers a comprehensive overview of current knowledge, and existing gaps, in sleep regulation and its functions, and the dynamics of brain activity during sleep across species. World-leading experts in the field will guide participants through the latest advancements.

The course features hands-on training across a variety of cutting-edge approaches, including:

• In vivo calcium imaging
• Large-scale molecular measures
• Human high-density EEG recording
• Wearable technologies for sleep monitoring
• Electrophysiological recordings
• Advanced analysis of big data
• Computational modelling
• Comparative approach with a diversity of animal models

By applying these diverse techniques to sleep research, participants will significantly advance their knowledge in sleep science and master a wide array of advanced tools and methodologies.

Course directors

University of Bern, Switzerland

University of Bordeaux, France

University of Surrey, UK

Keynote Speakers

Will be announced soon!

Instructors

Will be announced soon!

Course Content and Techniques

Will be announced soon!

Bordeaux School of Neuroscience, France

Registration

Fee : 5 000 € (includes tuition fee, accommodation and meals)

Applications will open soon.

Interacting with Neural Circuits

Course overview

Understanding how neural circuit activity translates into behavior is a fundamental challenge in neuroscience. Tackling this issue requires detailed knowledge of neural circuit architecture, including cell types, connectivity, and the spatiotemporal dynamics of activity in the intact brain during behavior. Additionally, establishing causal relationships between cellular and circuit-level processes and behavioral outputs requires precise perturbation of specific circuit elements with both temporal and spatial precision.

This course will introduce cutting-edge anatomical, genetic, optical, electrophysiological, optogenetic, and pharmacogenetic approaches available for addressing these challenges. Faculty members will cover tool development and their applications across diverse model systems, including flies, mice and zebrafish. Students will gain a comprehensive understanding of the strengths and limitations of these techniques, equipping them to design and interpret experiments effectively.

Course Directors

Venue Management

Keynote Speakers

Instructors

Ben Judkewitz, Einstein Center for Neurosciences, Charité, Germany
Carolina Rezaval, University of Birmingham, UK
Carsen Stringer, HHMI Janelia, USA
Darcy Peterka, Columbia University, USA
Eugenia Chiappe, Champalimaud Foundation, Portugal
Francois St Pierre, Baylor College of Medicine, USA
Greg Jefferis, MRC Laboratory of Molecular Biology, UK
Gonzalo de Polavieja, Champalimaud Foundation, Portugal
Karel Svoboda, Allen Institute, USA
Lisa Fenk, Max Planck Institute for Biological Intelligence, Germany
Michael Orger, Champalimaud Foundation, Portugal
Marta Moita, Champalimaud Foundation, Portugal
Na Ji, University of California, USA
Nathalie Rochefort, University of Edinburgh, UK
Srinivas Turaga, HHMI Janelia, USA
Stan Heinze, Lund University, Sweden
Talmo Pereira, Salk Institute, USA
Thomas Akam, University of Oxford, UK
Tobias Rose, University of Bonn Medical Center, Germany
Troy Margrie, Sainsbury Wellcome Centre, UK
Valentina Emiliani, Vision Institute, France
Vanessa Ruta, Rockefeller University, USA

Alexandre Leitão, Champalimaud Foundation, Portugal
Bruno Cruz, Allen Institute, USA
Cecilia Herbert, Open Ephys, Portugal
Charlie Dowell, Rockefeller University, USA
Corinna Gebehart, Champalimaud Foundation, Portugal
Dario Campagner, Sainsbury Wellcome Centre, UK
Joao Marques, Champalimaud Foundation, Portugal
Jonathan Cook, Champalimaud Foundation, Portugal
Laura Silva, Champalimaud Foundation, Portugal
Mathias Loidolt, University College of London, UK
Rute Marques, Champalimaud Foundation, Portugal
Yaara Lefler, Sainsbury Wellcome Centre, UK

Course content

This course combines a lecture series led by top researchers from around the world with a practical “hands-on” introduction to the latest methods for probing neural circuits using fruit flies, zebrafish, and transgenic mice. The course will focus on circuit anatomy and connectivity, activity recording and manipulation, and the relationship between neural circuits and behavior.

As part of the course, each student will conduct a mini-project, working under the guidance and supervision of experienced researchers and teaching assistants. This approach ensures participants develop both theoretical knowledge and practical skills in modern neuroscience methodologies.

Techniques

Techniques used during the course include:

Fruit flies and Zebrafish

– Optogenetic manipulation with and without digital holography

– Behavior & population calcium imaging using 2-photon microscopy

Mice

– In vivo 2-photon and 3-photon imaging

– All-optical experiments (simultaneous 2-photon optogenetics and 2-photon imaging)

– 1-photon and 2-photon miniscope imaging

– Extracellular recordings of neural population activity using Neuropixels probes in head-fixed and freely behaving animals

– Closed-loop behavioural experiments

Champalimaud Centre for the Unknown, Portugal

Registration

Fee : 4 500 € (includes tuition fee, accommodation and meals)

Applications closed

The CAJAL programme offers 4 stipends per course (waived registration fee, not including travel expenses). Please apply through the course online application form. In order to identify candidates in real need of a stipend, any grant applicant is encouraged to first request funds from their lab, institution or government.

Kindly note that if you benefited from a Cajal stipend in the past, you are no longer eligible to receive this kind of funding. However other types of funding (such as partial travel grants from sponsors) might be made available after the participants selection pro- cess, depending on the course.

Sponsors

The Brain Prize Course: Advanced Techniques for Synapse Biology

Course overview

Synapses are sites of information transfer and storage in the brain. These specialised structures integrate complex signals and undergo functional changes that underlie the formation of memories. Synaptic dysfunction is associated with early stages of neurodegenerative disorders such as Alzheimer’s disease, and underlies neurodevelopmental disorders such as autism spectrum disorders and intellectual disability.

Studying synapse function and plasticity is key to understanding brain circuits that underlie behaviour, and to identify synaptic malfunction mechanisms underpinning brain diseases. This course will allow students to integrate theoretical and methodological concepts on synapse biology with hands-on experience on state-of-the art imaging, functional and computational methodologies. The course provides an in-depth understanding to many concepts such as synapse formation and maintenance, pre- and postsynaptic mechanisms, structural and functional synaptic plasticity, synaptic integration in neuronal networks and synaptopathies. Hands-on experimental projects conducted in small groups with the support of senior scientists will expose the students to methodologies at the forefront of research in this field.

Partner

Course Directors

Institut de Biologie de l’ENS, France

University of Bordeaux, France

Honorary lectures from Brain Prize Winners

Keynote Speakers

Corette Wierenga, Radboud Universiteit – Nijmegen, Netherlands
Franck Polleux, Columbia University, New York, USA
Monica Di Luca, Università degli Studi di Milano, Italy
Nelson Rebola, Institut du Cerveau, Paris, France
Patrik Verstreken, VIB-KU Leuven Center for Brain & Disease Research, Belgium
Peter Scheiffele, Universität Basel, Switzerland

Instructors

Lynette Lim, VIB-KU Leuven Center for Brain & Disease Research, Belgiuim
Oriane Mauger, Max Planck Institute of Psychiatry – Frankfurt, Germany
Melissa Herman, Charité Berlin, Germany
Etienne Herzog, Interdisciplinary Institute for Neuroscience – Bordeaux, France
Lise Schwab, Interdisciplinary Institute for Neuroscience – Bordeaux, France
Audrey Dufau, Interdisciplinary Institute for Neuroscience – Bordeaux, France
Vasika Venugopal, Interdisciplinary Institute for Neuroscience – Bordeaux, France
Margaux Saint-Martin, Interdisciplinary Institute for Neuroscience – Bordeaux, France
Melissa Cizeron, Mechanisms in Integrated Life Sciences – Lyon, France
Corette Wierenga, Radboud Universiteit – Nijmegen, Netherlands
Ségolène Bompierre, Radboud Universiteit – Nijmegen, Netherlands
Chao Sun, Aarhus University, Denmark
Silvia Turchetto, Aarhus University, Denmark
Cyril Hanus, Institute for Psychiatry and Neurosciences of Paris, France
Matteo Fossati, CNR Institute of Neuroscience – Milano, Italy
Anne-Sophie Hafner, Radboud Universiteit – Nijmegen, Netherlands
Akshay Kapadia, Radboud Universiteit – Nijmegen, Netherlands
Emilie Pacary, Neurocentre Magendie – Bordeaux, France
Estelle Cartier, Neurocentre Magendie – Bordeaux, France
Dominique Fernandes, Interdisciplinary Institute for Neuroscience – Bordeaux, France
Romain Boularand, Interdisciplinary Institute for Neuroscience – Bordeaux, France
Ivo Calaresu, Interdisciplinary Institute for Neuroscience – Bordeaux, France
Camille Mergaux, Interdisciplinary Institute for Neuroscience – Bordeaux, France
Olivier Rossier, Interdisciplinary Institute for Neuroscience – Bordeaux, France,
Amine Mehidi, Interdisciplinary Institute for Neuroscience – Bordeaux, France
Florelle Domart, Interdisciplinary Institute for Neuroscience – Bordeaux, France
Simon Lecomte, Interdisciplinary Institute for Neuroscience – Bordeaux, France
Pauline Belzanne, Interdisciplinary Institute for Neuroscience – Bordeaux, France
Meera Chandra, Interdisciplinary Institute for Neuroscience – Bordeaux, France
Viviana Villicana Munoz, Interdisciplinary Institute for Neuroscience – Bordeaux, France

Course format

Three weeks of intensive training, with students in the lead, supported by senior scientists

The course includes both lectures by leading scientists in synapse biology, and hands-on training in two projects of about 9 days each, supported by senior scientists. Students (20 maximum) will attend theoretical and methodological lectures during the morning sessions, and spend the afternoon period in the Neuroscience Training Lab at the Neurocampus performing projects in groups of 2-3 students. The training laboratory is dedicated to the course and it is equipped with a wet lab for cellular and molecular biology, cell culture and animal rooms, electrophysiology rigs and behavior set-ups. Students will have access to core facilities at the University of Bordeaux, including to the Bordeaux Imaging Center, the Functional Genomics and the Biochemistry facilities. Support and expertise to carry out the projects is provided by external instructors coming from leading international laboratories in synapse biology, who will be present throughout the duration of the projects and assist students in their experiments (one instructor per group). Students are encouraged to participate in the design of projects, ahead of the course, through interaction with their project instructor. Students are welcome to bring their constructs or models, to be integrated in the project to be conducted. At the end of each project, students will present their findings and discuss with colleagues and instructors. Extracurricular activities (such as panel discussions on ethics, diversity and equity in Neuroscience), outreach activities and social events are also planned.

Course Topics

1. Activity-dependent regulation of gene expression and synapses

2. Local protein synthesis and degradation

3. Trafficking of synaptic proteins

4. Synaptogenesis and synaptic plasticity

5. Extracellular synaptic organizers, synaptic adhesion and circuit specification

6. Synaptic integration in neuronal networks

7. Presynaptic and postsynaptic mechanisms

8. Excitation and inhibition

9. Synaptic dysfunction in diseases

10. Structure-function of synaptic proteins

11. Neuromodulation

12. Human-specific regulations of synapses

Techniques

Super-resolution microscopy (PALM, STORM, DNA PAINT, STED)
Synapse-type specific proteomics (FASS)
Single-molecule RNA FISH, real-time qPCR
Stereotaxic surgery, in utero and single cell electroporation
Two photon and confocal microscopy, live imaging
FRET measurements for activity sensors
In vivo FRAP
Whole cell patch clamp recordings
Expansion microscopy
Electron microscopy
Computational analysis
Optogenetics
Gene editing
Behavior

Experimental Projects

Developmental trajectories of long-range GABAergic neurons
Exploration of RNA mechanisms underlying memory formation
Investigating mechanisms of low-frequency synaptic depression in cultured hippocampal synapses
How shearing forces impact multipartite synapses during synaptosome preparation and sorting
Visualizing Astrocyte-Neuron and Astrocyte-Synapse Interactions in 3D Using Expansion Microscopy
Imaging extracellular synapse organizers using live and super-resolution microscopy in the nematode Caenorhabditis elegans
Lighting up neuromodulation: visualizing PKA signaling in hippocampal neurons using a FRET-based imaging approach
Visualizing Activity-dependent Signaling for Synaptic Protein Clearance
Atomistic modeling of glycosylated synaptic protein structure
Assessing excitatory and inhibitory synapse development upon in vivo manipulation of gene function in distinct neuronal populations
Impact of local APP amyloidogenic proteolysis on presynaptic function
Analysis of excitatory and inhibitoy synapses in vivo using in utero electropration and stereotaxic injections
Exploring the impact of extracellular matrix complexity in the diffusion of circulating molecules and cell surface proteins
Revealing the role and localization of talin in glutamatergic synapses
Revealing the co-organization of synaptic proteins using SMLM microscopy techniques
Optically controlling synaptic transmission at hippocampal mossy fiber synapses with a bistable inhibitory optoGPCR

Bordeaux School of Neuroscience, France

Registration

Fee : 4 500 € (includes tuition fee, accommodation and meals)

Applications closed

Sponsors

NeuroAI – Neuroscience and AI

Course overview

Modern deep learning methods provide some of the best tools to model behavior and brain function today. Excitingly, AI systems have become the first artificial models capable of matching human performance in sophisticated cognitive tasks, such as visual recognition, language processing, and strategic planning. This unique capability makes them a key test bed for neuroscience research: by studying how these AI systems solve complex problems, we can generate and test hypotheses about the computational principles that biological brains might use. Moreover, thanks to amazing progress in neuroscientific experimental recording techniques over the last decade, we now have access to vast amounts of complex data, which can be used in computational modeling, across multiple modalities – from neural activity of thousands of neurons, to anatomical details of neuronal circuits, to whole brain neural recordings during complex behavior of humans and animals. These exciting developments—in both AI methodology and neuroscientific recordings—have inspired an emerging area of research at the intersection of neuroscience and AI.

The course gives a hands-on introduction to modern AI methods, including deep learning, and how it can be used for analyzing and modeling brain activity and behavior. Experts in the field will teach the basics of AI, and how to use them as models of the brain, cognition, and behavior.

Course Directors

Georg August University Göttingen, Germany

Johns Hopkins University, USA

Max Planck Institute for Software Systems, Germany

HHMI Janelia Research Campus, USA

Course Faculty

Jacob Yates – Berkley, USA
Martin Schrimpf – EPFL, Switzerland
Kevin Miller – Google DeepMind, UK
Patrick Mineault – Amaranth Foundation, USA
Carsen Stringer – HHMI Janelia Research Campus, USA
Chris Summerfield – Oxford University, UK
John Krakauer – Champalimaud, Portugal
Memming Park – Champalimaud, Portugal
Andreas Tolias – Stanford, USA
Jonathan Pillow – Princeton University, USA
Shailee Jain – UC San Fransisco, USA
Rui Ponte Costa, University of Oxford, UK

Instructors

Janne Lappalainen – University Tübingen, Germany
Farah (Fengtong) Du – HHMI Janelia Research Campus, USA
Mathis Pink – MPI Software Systems, Germany
Manasi Malik – Johns Hopkins University, USA

Course Content

Programme

The first two weeks will consist of full day hands-on lectures and tutorials from introductory to more advanced topics. The third week is reserved for more extensive group research projects.

First week

Introduction to NeuroAI and primer on deep learning for computer vision and language
Neural network models of vision and calcium imaging
Models for neuronal dynamics
Data-driven models of visual cortex during active vision
Understanding choice behavior using reinforcement learning models

Second week

Engineering a less intelligent AI (the fly)
System models of vision and language in the primate brain
Skill, practice, plasticity, and the cognitive-motor interface
Foundation models in neuroscience

Third week

The third week has lectures on more advanced topics. The remainder of the days are focused on project work.

Confirmed talks in the third week are:

Learning and generalization in human and neural networks
Engineering a less artificial intelligence

Students will design projects applying machine learning methods to neural recording and behavioral data sets.

Datasets

We encourage course faculty to bring datasets that can be used for projects. Here are some examples of datasets that will be available for project work

Calcium imaging data from mouse primary visual cortex in response to natural images and videos from the SENSORIUM competitions 2022 and 2023
Large dataset of human choices on a 4-armed drifting bandit task.
Data from foveal V1 of free-viewing marmosets along with continuously monitored gaze. Data from Marmoset retina with the same eye traces.
Publicly available data from the Brain-Score benchmark (vision and language). The vision data include non-human and human primate electrophysiology and fMRI recordings spanning the visual ventral stream and associated object recognition behaviors. The language data are human neuroimaging and reading time measurements. Meta-data from thousands of model alignment scores on all of the Brain-Score benchmarks.
A dataset with over 29,000 neurons responding to up to 65,000 natural image presentations in mouse V1. The neurons were expressing jGCaMP8s and we recorded their activity using two-photon calcium imaging at a rate of 30Hz.
Neuropixels speech dataset comprising spiking activity from >500 single neurons in awake human participants undergoing brain surgery. Neurons were recorded while participants listened to simple English sentences. Associated metadata for each neuron such as its anatomical position along the superior temporal gyrus and cortical depth will also be provided.

Techniques

Through hands on tutorials and project work, students will have the opportunities to learn about computational approaches in NeuroAI such as:

Deep learning models for vision and language (CNNs, transformers)
Reinforcement learning algorithms
State space models for neuronal time series
Machine learning for biophysical models of neuronal circuits

Champalimaud Centre for the Unknown, Portugal

Registration

Fee : 3 500 € (includes tuition fee, accommodation and meals)

Applications are closed.

Sponsors

Cancer Neuroscience

Course overview

Cancer neuroscience represents an interdisciplinary field at the forefront of cancer research, seamlessly combining insights from neurobiology and oncology. The intricate interplay between the nervous system and cancer has yielded profound insights into the mechanisms of tumor progression and the tumor microenvironment. The latter, comprising neuro-glial, immune, and endothelial networks, has been identified as a critical determinant of cancer growth and metastasis.

Cutting-edge technologies inspired by the neuroscience field are transforming our ability to study brain cancers from a neural perspective. This course will enable students to integrate theoretical and methodological concepts in neuro-oncology, combining modern neuroscience approaches with hands-on experience in state-of-the-art methodologies. The course provides an integrated understanding of the crosstalk between neuro-oncology and neuroscience.

Course Directors

Luxembourg Institute of Health, Luxembourg

Bordeaux Institute of Oncology – INSERM, France

German Cancer Research Center, Germany

Honorary Lecture - Brain Prize Winner

German Cancer Research Center, Germany

Keynote Speakers

Thomas Daubon, Institut de Biochimie et Génétique Cellulaires, France

Manuel Valiente, Centro Nacional de Investigaciones Oncológicas, Spain

Simona Parrinello, UCL Cancer Institute, UK

Aurélie Tchoghandjian, Institut de Neurophysiopathologie, France

Helene Castel, Laboratoire de Différenciation et Communication Neuronale et Neuroendocrine, France

Hrvoye Miletic, University of Bergen, Norway

Vidhya Madapusi Ravi, Freiburg Institute for Advanced Studies , Germany

Leila Akkari, Netherlands Cancer Institute, Netherlands

Dieter Henrik Heiland, Department of Neurosurgery, Germany

Elena Ciaglia, Università di Salerno, Italy

Instructors

Ahmad Charanek – Bordeaux Institute of Oncology, France
Audrey Burban – Institut de Biochimie et Génétique Cellulaires, France
Aurélie Tchoghandjia – Institut de Neurophysiopathologie, France
Bastien Redon – Neurocentre Magendie, France
Beatrice Senigagliesi – Interdisciplinary Institute for NeuroScience: Bordeaux, France
Benjamin Chauvineau – NutriNeuro, France
Camille Humeau – Bordeaux Institute of Oncology, France
Chiara Bastiancich – Institut de Neurophysiopathologie, France
Claire Larrieu – Institut de Biochimie et Génétique Cellulaires, France
Clement Morgat – Institut de Neurosciences Cognitives et Intégratives d’Aquitaine, France
Clementine Bosch Bouju – NutriNeuro, France
Cloe Tessier – Bordeaux Institute of Oncology
Doriane Bomont – Institut de Biochimie et Génétique Cellulaires, France
Ekin Reyhan – Universität Heidelberg, Germany
Emanuelle Georget – Bordeaux Institute of Oncology
Kevin Boye – Paris Cardiovascular Research Center, France
Kirill Smirnov – Institut de Psychiatrie et Neurosciences de Paris, France
Lucie Brisson – Bordeaux Institute of Oncology, France
Mahsa Rezaeipour – Luxembourg Institute of Health, Luxembourg
Maialen Arrieta – Institut de Biochimie et Génétique Cellulaires, France
Maria Haykal – Institut de Biochimie et Génétique Cellulaires, France
Mathis Pinglaut – Institut de Biochimie et Génétique Cellulaires, France
Nassim Haffiane – Interdisciplinary Institute for NeuroScience: Bordeaux, France
Oceane Martin – Institut de Biochimie et Génétique Cellulaires, France
Pilar Moreno-Sanchez – Luxembourg Institute of Health, Luxembourg
Stella Soyka – Universität Heidelberg, Germany
Thomas Daubon – Institut de Biochimie et Génétique Cellulaires, France
Valentina Lopardo – Università di Salerno, Italy

Course Content and Techniques

Cultures of brain tumor cells

Primary cultures of neurons, astrocytes, and oligodendrocytes

Primary culture of enteric nervous system cells (ENS) and ex vivo analysis of ENS structure in mouse models

Tumor cell spheroid cultures

Organoids

Organotypic brain slices

Co-culture of tumor cells with brain cells

Culture of glioblastoma cells in 3D-living systems of brain

Stereotaxic surgery for tumor implantation

Tumor debulking via the biopsy punch technique

Live imaging of cell-cell interactions

Confocal microscopy

Spinning-disk microscopy

Super-resolution microscopy

Two-photon microscopy

Multiphoton longitudinal imaging of tumor progression

DREADD manipulation and calcium imaging in mice during reward-based navigation.

Neuronal calcium activity using a head-mounted miniature microscope on animals performing behavioral tasks

Magnetic Resonance Imaging

Radiolabeling with radiometals and characterization of radio pharmaceuticals

SPECT/CT imaging and post-mortem biodistribution

PBMC isolation from human blood

Isolation of murine tumor-infiltrating immune cells

Characterization of immune cells by flow cytometry

High resolution respirometry using Resipher system and Oroboros Oxygraph-2k

Isolation of proteins and exosomes.

PamGene Technology

Methods to induce Blood-brain barrier opening in brain tumor models

Electrophysiology in multielectrode array

Electrophysiological patch-clamp recordings

Introduction to signal preprocessing, spike detection, and activity mapping

Image analysis using Imaris software

Analysis of cell motility with ImageJ

Analysis of spatial transcriptomics datasets using Seurat, Squidpy, R and Python

Analysis of 10x Genomics Visium datasets from human glioblastoma samples

Exploration of 10x Genomics Xenium imaging-based spatial data

Bordeaux School of Neuroscience, France

Registration

Fee : 4 500 € (includes tuition fee, accommodation and meals)

Applications are closed.

Sponsors

Neuroimmunology in Physiology and Disease: From Fundamental Concepts to Hands-on Training

Course Overview

The Cajal Course on Neuroimmunology will provide a comprehensive overview of the interactions between the nervous and immune systems, with a focus on microglia, macrophages, and adaptive immunity. The program will cover both physiological and pathological aspects, exploring the roles of microglia in brain homeostasis, their response to injury, and their involvement in neurodegenerative diseases. Sessions on macrophages will address their functions in the central and peripheral nervous systems, highlighting their contributions to neuroinflammation and tissue repair. The adaptive immune system’s influence on neurological conditions will also be discussed, including T and B cell responses in autoimmunity and neurodegeneration. The course will finally cover a session on body-brain interaction and the glymphatic system, in health and disease.

Combining lectures from leading experts in the field with advanced hands-on training, this course will cover a variety of approaches, including immune cell profiling by flow cytometry and histology, metabolic investigations, imaging techniques, in different in vitro and in vivo models, such as primary immune cells, iPSC-derived microglia and preclinical mouse models.

Course Directors

University of Lausanne, Switzerland

University of Bordeaux, France

University of Cambridge, UK

Keynote Speakers

Aleksandra Deczkowska, Institut Pasteur, Paris, France
Sonia Garel, Institut de Biologie de l’École Normale Supérieure Paris, France
Andrew Greenhalgh, University of Manchester, Manchester, UK
Laurent Groc, University of Bordeaux, CNRS, Bordeaux, France
Michael Heneka, Luxemburg University, Luxemburg
Jonathan Kipnis, Washington University School of Medicine, USA
Arthur Liesz, Ludwig-Maximilians Munich University, Germany
Marco Prinz, Freiburg University, Germany
Rejane Rua, Centre d’Immunologie de Marseille Luminy, France
Michal Schwartz, Weizmann Institute of Science, Israel

Instructors

Elena Avignone, Neurocampus Bordeaux, France
Pavle Boskovic, Washington University School of Medicine, USA
Amy Dashwood, Cambridge University, UK
Mohamad El Amki, University of Zurich, Switzerland
Max Fliegauf, University of Freiburg, Germany
Mariangeles Kovacs-Arevalo, Pasteur Institut, France
Saudina Mateus Gomes, Aix-Marseille Université, France
Charlotte Madore, University of Bordeaux, France
Renzo Mancuso, VIP Antwerp, Belgium
Katia Monsorno, University of Lausanne, Switzerland
Katerina Palios, Cambridge University, UK
Luca Peruzzotti-Jametti, Cambridge University, UK
Audrey Romano, Aix-Marseille Université, France
Alanna Spiteri, VIB Antwerp, Belgium
Daan Verhaege, Washington University School of Medicine, USA

Course Topics

Several different techniques and models will be used, including flow cytometry, fluorescence- and magnetic-activated cell sorting (FACS and MACS), confocal microscopy, high resolution respirometry, live imaging, electrophysiology, human iPSC-derived microglia, in vivo mouse models, murine primary cultures.

Course topics will include:

Microglia in the healthy and diseased brain
CNS-associated macrophages in physiology and pathology
Adaptive immunity and CNS interactions
The glymphatic system and brain immunity
Neuroimmune interactions in body-brain communication

Bordeaux School of Neuroscience, France

Registration

Fee : 4.000 € (includes tuition fee, accommodation and meals)

Applications closed

Course overview

Course directors

Giuseppe Testa

Flora Vaccarino

Scientific Directors

Nicolò Caporale

Soraya Scuderi

Emanuele Villa

Keynote Speakers

Instructors

Course content

Topics

Aims and Techniques

Bordeaux School of Neuroscience, France

Registration

Course overview

Course directors

Keynote speakers

Instructors

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Course format

Champalimaud Centre for the Unknown, Portugal

Registration

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Gioele La Manno

Hannah Hochgerner

Alexandre Favereaux

Keynote Speakers

Instructors

Course Content and Techniques

Learning Objectives

Course Structure

Bordeaux School of Neuroscience, France

Registration

Course overview

Course directors

Jerome Badaut

Robert G. Thorne

Keynote Speakers

Instructors

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Projects

Bordeaux School of Neuroscience, France

Registration

Course overview

Course directors

Carolina Gutierrez Herrera

Arthur Leblois

Julie Seibt

Keynote Speakers

Instructors

Course Content and Techniques

Bordeaux School of Neuroscience, France

Registration

Course overview

Course Directors

Venue Management

Keynote Speakers

Instructors

Course content

Techniques

Champalimaud Centre for the Unknown, Portugal

Registration

Sponsors

Course overview

Partner

Course Directors

Honorary lectures from Brain Prize Winners

Erin Schuman

Michael Greenberg

Keynote Speakers

Instructors

Course format

Course Topics

Techniques

Experimental Projects

Bordeaux School of Neuroscience, France

Registration

Sponsors