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Machine Learning/Articfical intelligence course

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. This course provides 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 data representations of behavior, dissect them statistically, model their dynamics, and integrate behavioral measurements with other kinds of neurobiological data. 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.

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, see below) we will use two main experimental model systems: flies (Drosophila melanogaster) and zebrafish (Danio rerio). Several days of instruction will focus on analysis of video data, and on these days, students may use videos of flies and fish, videos we provide of mammals behaving, or videos of their own organism of choice. In the student project portion of the course (block 3), students may use these experimental organisms, as well as, subject to their availability, organisms in use at the Champalimaud.

We will cover data acquisition (software, hardware, tools), preprocessing (single animal, body parts and multiple animals tracking systems), data analysis (clustering, ethograms) and modeling.

Course directors

Gordon Berman

Course Director

Emory University, USA

Benjamin de Bivort

Course Director

Harvard University, USA

Champalimaud Foundation, Portugal

Orit Peleg

Course Director

University of Colorado, USA

Greg Stephens

Course Director

VU University Amsterdam, The Netherlands
OIST Graduate University, Japan

Keynote speakers

Sama Ahmed, University of Washington, USA
Kristin Branson – hhmi, Janelia Research Campus, USA
Bing BruntonUniversity of Washington, USA
António C. Costa, Ecole Normale Supérieure de Paris, France
Serena Ding – Max Planck Institute of Animal Behavior, Germany
Giorgio Gilestro – Imperial College London, UK
Alex JordanMax Planck Institute of Animal Behavior, Germany
Ilona KadowTechnical University of Munich, Germany
Ann KennedyNorthwestern University, USA
Natasha Mhatre Western University, Canada
Mala Murthy, Princeton University, USA
Ilya NemenmanEmory University, USA
Talmo Pereira – Salk Institute for Biological Studies, USA
Sam ReiterOkinawa Institute of Science and Technology, Japan
Barbara WebbUniversity of Edinburgh, UK

Instructors

Tosif Ahamed – Mount Sinai Hospital, Toronto, Canada
Jake GravingMax Planck Institute of Animal Behavior, Germany
Kanishk JainEmory University, USA
Ugne Klibaite – Center for Brain Science, Harvard University, USA
Chantal Nguyen – BioFrontiers Institute, University of Colorado Boulder, USA
Denise Yoon, Harvard University, USA
Adrien Jouary, Champalimaud Foundation, Portugal
Dean Rance, Champalimaud Foundation, Portugal
Francisco Romero, Veriff, Spain
Bruno Cruz, NeuroGEARS, UK

Course content

Projects

Projects from previous years:

  • The role of visual cues in social behaviour in flies;
  • Social learning in Drosophila melanogaster;
  • Mapping the behavioural repertoire of zebrafish larvae in response to tastants and neuroactive compounds;
  • Slfish: characterizing the collective behavior of larval zebrafish following acute social isolation;
  • Skinner’s flies: inducing superstitious microbehaviors via random operant rewards;
  • The role of lateralized latency asymmetry in virtual task performance;

Ideas for projects for the upcoming course:

  • Manifolds in dynamical representations of behavior;
  • Deep attention models of collective fish behavior;
  • Modelling behavior with different tradeoffs of accuracy and complexity using symbolic regression;
  • Unsupervised discovery of motifs in rodent vocalizations.
QAB 2

For more information on the course programme, you can visit the past course website.

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 : 3.500 € (includes tuition fee, accommodation and meals)

Applications closed on 20th December 2021

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.

Bioenergetics for Brain Function

Course overview

The brain is one of the most energy-consuming organs of the body. Indeed, one could say that the main difference between the brain and a computer is the plug: once plugged, energy is not an issue for the computer, but it is a constant burden for each cell of the brain. As such, energy metabolism in the brain is not just a mere housekeeping and survival service, but it constitutes an essential element directly participating in signaling, computation and behavior.

This course will address the different ways by which energy metabolism participates to high-order brain functions and the underlying cellular, molecular and circuit mechanisms.

Course directors

Juan Pedro Bolaños

Course director

University of Salamanca,

Spain

NeuroCentre Magendie – INSERM
University of Bordeaux
France

Centre RMSB – CNRS
University of Bordeaux
France

Keynote Speakers

Felipe Barros – Centro de Estudios Cientificos, Valdivia, Chile
Juan Pedro Bolaños – University of Salamanca, Spain
Gilles Bonvento – CNRS, MIRCen, Paris, France
Anne-Karine Bouzier-Sore – CNRS, Centre RMSB, Bordeaux, France
Daniela CotaINSERM, Neurocentre Magendie, Bordeaux, France
Jaime De Juan-Sanz – Institut du Cerveau, Paris, France
Stephanie Fulton – University of Montreal, Canada
Ralf Jockers – Inserm, Institut Cochin, Paris, France
Giovanni Marsicano – INSERM, Neurocentre Magendie, Bordeaux, France
Aude Panatier – INSERM, Neurocentre Magendie, Bordeaux, France
Luc Pellerin – IRTOMIT, Poitiers, France
Carmen Sandi – EPFL, Lausanne, Switzerland

Instructors

Felipe Baeza-Lehnert – University of Leipzig, Germany + Centro de Estudios Científicos, Valdivia, Chile
Jerome Baufreton – University of Bordeaux, France
Luigi Bellocchio – University of Bordeaux, France
Giovanni Bénard – MRGM Laboratoty, Bordeaux, France
Abel Eraso Pichot – University of Bordeaux, France
Ignacio Fernandez-Moncada – University of Bordeaux, France
Marina Garcia Macia – University of Salamanca, Spain
Anna Hadjichambi – Institute of Hepathology, London, UK
Morgane Jego – University of Bordeaux, France
Daniel Jimenez – University of Salamanca, Spain
Christos Konstantinou – Institute of Hepathology, London, UK
Rodrigo Lerchundi – MIRCen, CNRS, Paris, France
Shingo Nakajima – University of Montreal, Canada
Antonio Pagano-Zottola – Institut de Biochimie Génétique et Cellulaires, Bordeaux, France
Sandrine Pouvreau – University of Bordeaux, France
Rubén Quintana-Cabrera – University of Salamanca, Spain

Course content

Topics & Techniques

The following techniques will be covered during the course:

  1. Cultures of mouse primary astrocytes and neurons.
  2. Bioenergetic profiles in mouse primary astrocytes and neurons using the Seahorse equipment.
  3. Isolation of neurons and astrocytes from adult mice using immunomagnetic approach.
  4. Flow cytometric analysis of mitochondrial membrane potential and mitochondrial ROS production in cultured primary brain cells and in acute immunomagnetically isolated brain cells.
  5. Purification of mitochondrial fraction using differential centrifugation and immunomagnetic mitochondrial isolation approach.
  6. Analysis of the mitochondrial respiratory chain organization using blue native gel electrophoresis from mitochondria isolated from either cultured cells, acutely isolated brain cells and brain-specific regions.
  7. Study of real-time changes in mitochondrial membrane potential using confocal microscopy in cells expressing genetic ATP and ROS probes.
  8. Classical techniques for the determination of common energy metabolites and enzyme activities in including the MRC complexes
  9. Glucose and lactate metabolism in neurons: comparison of [1-13C]glucose and [3-13C]lactate metabolism in neuronal cultures, followed by 13C-NMR spectroscopy.
  10. Glucose and lactate metabolism in astrocytes : comparison of [1-13C]glucose and [3-13C]lactate metabolism in astrocytic cultures, followed by 13C-NMR spectroscopy.
  11. Metabolic changes during brain activity: in vivo functional MRI and MRS during whisker stimulation: visualisation of the barrel cortex and quantification of the lactate increase during brain activity in rat
  12. Impact of metabolism for neuroprotection: longitudinal study (diffusion MRI) to follow brain lesions and regression following different injected substrates (pyruvate, glucose, lactate etc…)
  13. Electrophysiology of hippocampal and cortical slices: comparison of population spike amplitudes and duration of activity with different substrates (glucose, ketone bodies, lactate, glucose+lactate…)
  14. Analysis of mitochondrial respiration in ex vivo brain areas using the Oroboros technology
  15. Mitochondrial calcium analysis by in vitro and in vivo imaging using Fiber photometry
  16. Use of metabolic biosensors by in vitro and in vivo imaging using Fiber photometry
  17. Impact of modulation of brain mitochondrial metabolism on behavior in mouse
  18. Investigation of mitochondrial proteins trafficking using unconventional genetic tools
  19. Impact of brain mitochondrial activity on whole-body energy balance.

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 : 3.500 € (includes tuition fee, accommodation and meals)

Application closed on 1 March 2021

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.

COVID-19 update: in case the Bioenergetics for Brain Function course is postponed due to the pandemic, all applicants will have the choice to maintain their application or cancel it. Applicants who were already selected to attend will not have to reapply and will automatically be enrolled in the rescheduled course.

In addition, the Cajal Programme will not, as far as possible, request the registration fee from selected applicants until the course has been secured and confirmed. Nevertheless, should the course be cancelled before the course dates and the registration fees already collected, participants will be reimbursed.

Course sponsors

Ageing cognition

Course overview

The normal aging process is associated with reduced performance on cognitive tasks that require one to quickly process or transform information to make a decision, including measures of speed of processing, executive cognitive function, working and relational memories. Structural and functional alterations in the brain correlate with these age-related cognitive changes, such as loss of synapses, and dysfunction of neuronal networks. It is crucial to develop new approaches that consider the whole neuroanatomical, endocrine, immunological, vascular and cellular changes impacting on cognition.

This 3-week course will cover the fundamentals of cognitive aging -including inter-individual differences, cognitive and brain reserve and risk factors- and highlight the newest functional imaging methods to study human brain function. The Faculty will share the state-of-the-art molecular, optical, computational, electrophysiological, behavioral and epidemiological approaches available for studying the aging brain in diverse model systems.

Students will learn the potential and limitations of these methods, through practical experience in a combination of lectures addressing aging in both humans and animal models and hands-on-projects. They will acquire sufficient practical experience to model, design and interpret experiments and brainstorm on novel technologies and hypotheses to explore the aging of the brain using more integrative and creative approaches.

Course directors

Luísa V. Lopes

Course Director

Neurobiology of Ageing & Disease
iMM Lisboa
Portugal

Cheryl L. Grady

Co-director

The Rotman Research Institute, Baycrest
& University Toronto
Canada

Nora Abrous

Co-director

Neurocentre Magendie
INSERM U 1215 – University of Bordeaux
France

Keynote Speakers

Hélène Amieva – Bordeaux population Health Center, France
Adam Antebi – Max Planck Institute for Biology of Ageing, Germany
Carol Barnes – University of Arizona, USA
Luc Buée – University of Lille, France
Gwenaëlle Catheline – INCIA, Bordeaux, France
Maria Llorens-Martin – Universidad Autonoma Madrid, Spain
Aline Marighetto – Neurocentre Magendie, Bordeaux, France
Lars Nyberg – Umeå University, Sweden
Laure Rondi-Reig – Sorbonne Université, Paris, France
Yaakov Stern Columbia University, USA

Instructors

Claudia Almeida – CEDOC, UNL, Lisbon, Portugal
Nicolas Blin – Neurocentre Magendie, Bordeaux, France
Vanessa Charrier – Neurocentre Magendie, Bordeaux, France
Joana Coelho – IMM, Lisbon, Portugal
Miguel De la Flor Garcia – Universidad Autónoma de Madrid , Spain
Nicole Etchamendy – Neurocentre Magendie, Bordeaux, France
David Koss – University of New castle, UK
Nuno Morais – IMM, Lisbon, Portugal
Paula Pousinha – IPMC, Nice, France
Miguel Remondes – IMM, Lisbon, Portugal
Jenny Rieck – Baycrest & Univ. Toronto,
Azza Sellami – Neurocentre Magendie, Bordeaux, France
Jean Vincent – Sorbonne Université, Paris, France

Course content

Projects

The following projects are confirmed so far:

  • Project 1: Is lysosome dysfunction a mechanism of synapse aging?
  • Project 2: Physiological signatures of cognitive aging
  • Project 3: Recording neuronal activity on hippocampal slices from aged mice
  • Project 4: Inter-individual variability of declarative memory decline in healthy aging: a brain network analysis in humans based on a virtual radial-maze task.
  • Project 7: Immunohistochemistry on brain tissue obtained from aged humans and rodents
  • Project 8: Unveiling the transcriptomic signatures of human brain ageing
  • Project 9: In vivo optogenetic to manipulate adult neurogenesis
  • Project 10: Inducing Neurons (iNs) from human fibroblasts to preserved the cellular synaptic ageing-signature
  • Project 11 and 12: Inter-individual variability of declarative memory decline in healthy aging: a brain network analysis in mice on a radial-maze task.
  • Project 13 and 14: Quantification of cortical DNA damage in age-associated neurodegenerative diseases.

For more information on projects and techniques which will be taught at the course, download the projects list.

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 : 3.500 € (includes tuition fee, accommodation and meals)

Application closed on 21 June 2021

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.

Advanced imaging techniques for cellular and systems neuroscience (rescheduled)

Course overview

Rapid advances in live imaging of targeted cellular morphologies and functions underpin the emerging revolution in our understanding of synapses, circuits, and behaviour. This Cajal course will assemble, as international faculty, leading experts in developing and exploiting cutting-edge imaging techniques that have been propelling such advances. How to combine genetically encoded fluorescence labelling with behavioural designs, micro-circuit monitoring, or single-molecule tracking, how to avoid pitfalls of having false-positive observations and inherent noise, how to best analyse your multi-dimensional data will be, among others, the recurrent subjects of the course. An intense programme of lectures and seminars will be combined with supervised, hands-on practical training modules and group assignments using experimental setups and tools provided by the world-leading research environment of the Bordeaux School of Neuroscience.

Course partner

Dimitri Rusakov

Course Director

UCL Queen Square
Institute of Neurology
United Kingdom

Tatiana Korotkova

Co-Director

Neuronal circuits and behaviour
MPI for Metabolism Research
Germany

Grégory Giannone

Co-Director

CNRS, IINS UMR 5297
University of Bordeaux
France

Keynote speakers

Thomas Blanpied – University of Maryland School of Medicine, USA
Daniel Choquet – IINS, University of Bordeaux, France
Rosa Cossart – CNRS, Inserm – INMED, Aix-Marseille Université, France
Olga Garaschuk – University of Tuebingen, Germany
Laurent Groc – IINS, University of Bordeaux, France
Michael Hausser – University College London, UK
Christian Henneberger – University of Bonn, Germany
Christophe Leterrier – INP CNRS-AMU UMR 7051,
Aix-Marseille Université, France
Valentin Nagerl – University of Bordeaux, France
Tim Ryan – Weill Cornell Medical College, USA
Ilaria Testa – KTH Royal Institute of Technology, Sweden
Andrea Volterra – University of Lausanne, Switzerland
Kirill Volynski – University College London, UK

Instructors

Stephane Bancelin – University of Bordeaux, France
Francisco de los Santos – MPI Cologne, Germany
Yulia Dembitskaya – University of Bordeaux, France
Ani Jose – IINS, University of Bordeaux, France
Olga Kopach – University College London, UK
Philipe R. F. Mendonça – University College London, UK
Dragomir Milovanovic – Charité University Clinic, Berlin, Germany
Christian Hoffmann – Charité University Clinic, Berlin, Germany
Jakob Rentsch– Charité University Clinic, Berlin, Germany
Petr Unichenko – University College London, UK
Olga Tiurikova – University College London, UK
Hanna Van Den Munkhof – MPI Cologne, Germany
Kaiyu Zheng – University College London, UK
Olivier Nicole – IINS, University of Bordeaux, France
Julien Dupuis – IINS, University of Bordeaux, France
Xuesi Zhou – IINS, University of Bordeaux, France

Course content

                             Topics & Techniques

Students will learn:

– Super-resolved organisation of the synaptic cleft.

– Nanoscale monitoring and probing of NMDA receptors.

– Super-Resolution probing of the axonal initial segment.

– RESOLFT nanoscopy.

– Super-Resolution Imaging of Brain Nano-Structure In Vivo.

– Nanoscale imaging and manipulation of synapse function to study the brain.

– Monitoring molecular machinery of synaptic plasticity.

– Probing the molecular basis of synaptic transmission.

– Optical sensors for neurotransmitters.

– Multiplexed imaging of presynaptic function.

– Ca2+ regulation of synaptic vesicle fusion in central synapses.

– Optical monitoring of volume transmission.

– Studying astrocytes in synaptic function with 1D-to-3D two-photon Ca2+ imaging.

Projects

For more information on projects download the “Programme info”

  • Project 1: “Imaging prefrontal cortex neurons encoding social information”.
  • Project 2: “Imaging hippocampal place cells in freely moving animals”.
  • Project 3: “FRET imaging of NMDA receptor co-agonists dynamics”.
  • Project 4: “Assessing the mechanosensitive properties of the membrane periodic skeleton
    (MPS) in neurons”.
  • Project 5: “RESOLFT nanoscopy to study the fast reorganization of dendritic spines”.
  • Project 6: “Single synapse imaging of glutamate release and pre-synaptic Ca2+ for study of
    pre-synaptic receptor function and short-term synaptic plasticity”.
  • Project 7: “Quantitative intracellular calcium measurements using fluorescent lifetime
    imaging microscopy”.
  • Project 8: “A viral strategy for targeting and manipulating principal neurons: probing the
    glutamatergic synapse function at multi-synapse imaging approach”.
  • Project 9: “Probing of astroglial Ca2+ dynamics in organised brain tissue through
    fluorescent intensity and lifetime measurements”.
  • Project 10: “Multicolor multiphoton imaging of single synaptic release sites in vivo”.
  • Project 11: “High spatial-temporal imaging of a heterogeneous population of synapses in
    neuronal cultures using the iGluSnFR probe”.
  • Project 12: “Super-resolution shadow imaging in the mouse brain”.
  • Project 13: “Dual color single particle tracking to study membrane receptors dynamics”.
  • Project 14: “Imaging tripartite synapses using super-resolution microscopy”.
  • Project 15: “Nanoscale organization and dynamics of synapsin condensates”

For more information on projects and techniques which will be taught at the course, download the projects list.

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 : 3.500 € (includes tuition fee, accommodation and meals)

Application call closed on 5 July 2021

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.

Course sponsors

Neural circuit basis of computation and behaviour

Course overview

How does the activity of neural circuits govern information processing, enable memory formation, and give rise to behaviour? Tackling these questions is one of the great challenges in current neuroscience. To make progress, quantitative studies of both structure and function of neural circuits are required, which these days have become feasible with a collection of new and broad methods. Neural circuit research bridges the molecular-cellular level to the levels of large-scale brain operation and animal behaviour and thus promises to reveal principles of spatiotemporal circuit dynamics that underlie specific brain states and behaviours. The relevance and role of specific cell types and of local as well as long-range circuit motifs need to be understood. This course aims to bring students up-to-date with the most recent developments in this exciting and fundamental field of neuroscience research. The focus will be on the advanced experimental approaches that are available today for the dissection of neural circuit connectivity and activity in various animal models (mouse, fly, zebrafish).

The Cajal course is an intensive three-week course that guides participants through the theory and practice of state-of-the-art methods for addressing pertinent questions in this field of research. This course will teach the latest technological advances in optical, electrophysiological, genetic, viral tracing, anatomical, and optogenetic approaches for the study of neural circuits. Students will learn the current state of knowledge of how neural circuits are organized, especially in the mammalian mouse brain, and how information can be processed in biological circuits through population-based activity patterns. The faculty will consist of international experts in their respective fields, discussing fundamental concepts and their own research, introducing methods relevant for neural circuit research, and providing hands-on projects. Students will perform experimental projects to apply these methods to scientific problems, they will learn how to analyse acquired data, and they will discuss strengths and limitations of the various techniques. The course is designed for PhD students, postdoctoral researchers, and early-stage group leaders, and is aimed at providing them with an enhanced tool set for addressing their current and future research questions.

Course partner

Course directors

Fritjof Helmchen

Course Director

Brain Research Institute, University of Zurich, Switzerland

Andreas Frick

Co-Director

Neurocentre Magendie, INSERM U1215, University of Bordeaux, France

Cyril Herry

Co-Director

Neurocentre Magendie, INSERM U1215, University of Bordeaux, France

Keynote speakers

Antoine Adamantidis – University of Bern (Switzerland)
Athena Akrami – University College London (UK)
Matteo Carandini – University College London (UK)
Megan Carey – Champalimaud Research (Portugal)
Marie Carlen – Karolinska Institute (Sweden)
Valentina Emiliani – Vision Institute Paris (France)
Rainer Fiedrich – Friedrich Miescher Institute for Biomedical Research (Switzerland)
Nadine Gogolla – Max Planck Institute of Neurobiology (Germany)
Benjamin Grewe – ETH Zurich (Switzerland)
Johannes Kohl – Francis Crick Institute (UK)
Matthew E. Larkum – Humboldt University of Berlin (Germany)
Tommaso Patriarchi – University of Zurich (Switzerland)
Pavan Ramdya -EPFL Lausanne (Switzerland)
Nathalie Rochefort – The University of Edinburgh (UK)
Lisa Roux – Bordeaux Neurocampus (France)
Manuel Zimmer – University of Vienna (Austria)

Instructors

Jerôme Baufretton – Bordeaux Neurocampus (France)
Philipp Bethge – University of Zurich (Switzerland)
Roman Boehringer – ETH Zurich (Switzerland)
Cecilia Castelli – Bordeaux Neurocampus (France)
Simon d’Aquin – University of Zurich (Switzerland)
Lorena Delgado – Bordeaux Neurocampus (France)
Matthias Durrieu – EPFL (Switzerland)
Gabrielle Girardeau – Institut du Fer à Moulin (France)
Noelle Grosjean – Bordeaux Neurocampus (France)
Yann Humeau – Bordeaux Neurocampus (France)
Daniel Jercog – Bordeaux Neurocampus (France)
Jean-Sebastien Jouhanneau – MDC Berlin (Germany)
Marie Labouesse – ETH Zurich (Switzerland)
Frederic Lanore – Bordeaux Neurocampus (France)
Arthur Leblois – Bordeaux Neurocampus (France)
Christopher Lewis – University of Zurich (Switzerland)
Catherine Marneffe – Bordeaux Neurocampus (France)
Pavan Ramdya – EPFL (Switzerland)
Lisa Roux – Bordeaux Neurocampus (France)
Gwendolin Schoenfeld – University of Zurich (Switzerland)
Ourania Semelidou – Bordeaux Neurocampus (France)
Sandra Soukup – Bordeaux Neurocampus (France)
Naoya Takahashi – Bordeaux Neurocampus (France)
Roman Ursu – Bordeaux Neurocampus (France)
Nikita Vladimirov – University of Zurich (Switzerland)
Yuktiben Vyas – Bordeaux Neurocampus (France)
Nanci Winke – Bordeaux Neurocampus (France)
Jonathan Zapata (Inscopix)

Course content

Topics & Techniques

Participants will learn all basic requirements to perform:

ex vivo optogenetic and patchclamp recordings in acute brain slices;

in vivo calcium imaging experiments in freely moving mice using miniaturized microscopes;

– laser scanning lightsheet microscope by disassembling and reassembling a benchtop version of the mesoSPIM before preparing, acquiring and analysing various cleared neuronal samples;

– how to operate a two-photon microscope and how to do basic trouble-shooting;

– basics of electrode design, construction and instrumentation;

– basic requirements to perform extracellular recordings in singing birds using motorized micro-drive; basic procedures to image activity from individual dendrites of cortical pyramidal neurons in awake mice;

– basic spike data analysis (spike sorting, detection of tagged unit);

– dissection, microimplantation, and specimen preparation for live imaging; Calcium imaging data acquisition and computational data analysis;

Projects

The following projects are confirmed so far:

Project 1: “Imaging neural population activity along the gut-brain axis in adult Drosophila”

Project 2: “Two-photon targeted patch-clamp and calcium population imaging in mouse neocortex during tactile stimulation.”

Project 3: “Monitoring neuronal activity in the song-control circuits in freely behaving zebra finches.”

Project 4: “MesoSPIM light-sheet imaging of anatomical projections in the cleared mouse brain”

Project 5: “Functional Representations of Tactile Stimuli in the Cortex Using In Vivo 2-Photon Calcium Imaging”

Project 6: “Large scale multi-electrode recordings and optogenetic manipulations of neuronal subtypes in freely moving animals.”

Project 7: “All optical imaging and stimulation of neuromodulator release in freely moving mice (multiplex fiber photometry)”

Project 8: “Ex vivo optogenetic manipulations of basal ganglia circuits”

Project 9: “In vivo calcium imaging of hippocampal CA1 population activity in the freely moving mouse using miniaturized microscopes”

Project 10: “In vivo multimodal, multiscale physiology”

Project 11: “In vivo optogenetic manipulations of prefrontal circuits.”

Project 12: “Multi-site electrophysiological activities in a working memory task and related consolidation sleeping phases.”

Project 13: “Two-photon calcium imaging of cortical dendrites in awake head-fixed mice.

Project 14: ‘‘Birth of a memory: ex vivo optogenetic approach to study hippocampal engrams’’

Registration

Registration fee: €3.500,00 (includes tuition fee, accommodation and meals)

Application closed on 13th December 2021

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.

Quantitative Approaches to Behaviour

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. This course provides 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 data representations of behavior, dissect them statistically, model their dynamics, and integrate behavioral measurements with other kinds of neurobiological data. 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.

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, see below) we will use two main experimental model systems: flies (Drosophila melanogaster) and zebrafish (Danio rerio). Several days of instruction will focus on analysis of video data, and on these days, students may use videos of flies and fish, videos we provide of mammals behaving, or videos of their own organism of choice. In the student project portion of the course (block 3), students may use these experimental organisms, as well as, subject to their availability, organisms in use at the Champalimaud.

We will cover data acquisition (software, hardware, tools), preprocessing (single animal, body parts and multiple animals tracking systems), data analysis (clustering, ethograms) and modeling.

Course directors

Gordon Berman

Course Director

Emory University, USA

Benjamin de Bivort

Course Director

Harvard University, USA

Champalimaud Foundation, Portugal

Orit Peleg

Course Director

University of Colorado, USA

Greg Stephens

Course Director

VU University Amsterdam, The Netherlands
OIST Graduate University, Japan

Keynote speakers

Sama Ahmed, University of Washington, USA
Kristin Branson – hhmi, Janelia Research Campus, USA
Bing BruntonUniversity of Washington, USA
António C. Costa, Ecole Normale Supérieure de Paris, France
Serena Ding – Max Planck Institute of Animal Behavior, Germany
Giorgio Gilestro – Imperial College London, UK
Alex JordanMax Planck Institute of Animal Behavior, Germany
Ann KennedyNorthwestern University, USA
Natasha Mhatre Western University, Canada
Ilya NemenmanEmory University, USA
Talmo Pereira – Salk Institute for Biological Studies, USA
Sam ReiterOkinawa Institute of Science and Technology, Japan
Barbara WebbUniversity of Edinburgh, UK

Instructors

Tosif Ahamed – Mount Sinai Hospital, Toronto, Canada
Kanishk JainEmory University, USA
Ugne Klibaite – Center for Brain Science, Harvard University, USA
Chantal Nguyen – BioFrontiers Institute, University of Colorado Boulder, USA
Denise Yoon, Harvard University, USA
Adrien Jouary, Champalimaud Foundation, Portugal
Dean Rance, Champalimaud Foundation, Portugal
Francisco Romero, Veriff, Spain
Bruno Cruz, NeuroGEARS, UK

Course content

Schedule

Week 1

Sunday, May 22nd: Arrival & Welcome reception
Monday, May 23rd: Keynote lecture by Ben de Bivort / Afternoon tutorial: Build a rig & capture movies by Ben de Bivort & Giorgio Gilestro
Tuesday, May 24th: Keynote lecture by Giorgio Gilestro / Afternoon tutorial: Build a centroid tracker by Ben de Bivort & Giorgio Gilestro
Wednesday, May 25th: Keynote lecture by Alex Jordan / Afternoon tutorial: Multianimal idtracker.ai by Francisco Romero & Dean Rance
Thursday, May 26th: Morning tutorial by Gonzalo de Polavieja / Afternoon tutorial: Deep Learning notebooks applied to behaviour data sets by Gonzalo de Polavieja 
Friday, May 27th: Keynote lecture by Talmo Pereira / Afternoon tutorial: Limb and body tracking by Talmo Pereira

Week 2

Sunday, May 29th: Keynote lecture by Kristin Branson / Afternoon tutorial: Supervised classification by Kristin Branson
Monday, May 30th: Keynote Lecture by Sam Reiter / Afternoon tutorial: Dynamics of behaviour by Greg Stephens & Tosif Ahamed
Tuesday, May 31st: Keynote lecture by Ben de Bivort & Gordon Berman / Afternoon tutorial: Unsupervised analysis of behaviour by Ugne Klibaite & Kanishk Jain
Wednesday, June 1st: Keynote lecture by Orit Peleg / Afternoon tutorial: Probabilistic models by Bing Brunton
Thursday, June 2nd: Keynote lecture by Barbara Webb / Afternoon tutorial: Braitenberg and agent-based models by Barbara Webb & Orit Peleg
Friday, June 3rd: Keynote lecture by António Costa / Afternoon: Project design

Week 3

Sunday June 5th Keynote lecture by Ilya Nemenman / Afternoon: Project development
Monday, June 6th: Keynote lecture  by Serena Ding / Afternoon: Project development
Tuesday, June 7th: Keynote lecture by Ann Kennedy / Afternoon: Project development
Wednesday, June 8th: Keynote lecture by Natasha Mhatre / Afternoon: Project development
Thursday, June 9th: Keynote lecture by Sama Ahmed
Friday, June 10th: Project presentations
Saturday, June 11th: Departure

Projects

Projects from previous years:

  • The role of visual cues in social behaviour in flies;
  • Social learning in Drosophila melanogaster;
  • Mapping the behavioural repertoire of zebrafish larvae in response to tastants and neuroactive compounds;
  • Slfish: characterizing the collective behavior of larval zebrafish following acute social isolation;
  • Skinner’s flies: inducing superstitious microbehaviors via random operant rewards;
  • The role of lateralized latency asymmetry in virtual task performance;

Ideas for projects for the upcoming course:

  • Manifolds in dynamical representations of behavior;
  • Deep attention models of collective fish behavior;
  • Modelling behavior with different tradeoffs of accuracy and complexity using symbolic regression;
  • Unsupervised discovery of motifs in rodent vocalizations.
QAB 2

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 : 3.500 € (includes tuition fee, accommodation and meals)

Applications closed on 20th December 2021

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.

Single cell profiling and analysis in neuroscience

Course overview

Understanding the cellular complexity of the nervous system is a key endeavor in the pursuit to reveal the biological underpinnings of brain function. The recent methodological development of high-throughput single-cell profiling techniques and analysis has emerged as an essential tool for characterizing cellular diversity in the brain offering data sets that hold the promise of being complete, accurate and permanent. This course will teach central ideas, methods, and practices of single cell profiling and hands-on computational analysis through a combination of lectures from prominent international faculty speakers, experimental projects and data analysis workshops.

The course will include practical training in small groups of students on single cell methodologies and computational and statistical data analysis needed to interpret large data sets. This integration of data analysis with hands-on experiments will allow the students to gain knowledge in technical performance as well as biological interpretation of single cell data sets.

This advanced course is aimed for graduate students from a variety of disciplines, including neuroscience, physics, computer science and applied mathematics. Students are expected to have a keen interest and basic background in neurobiology, and to fully benefit from the data analysis it is expected that the students have at least a basic knowledge in programming.

Course partner

Course directors

Department of Medical Biochemistry and Biophysics,  Karolinska Institute,  Sweden

Biomedical Informatics, Harvard Medical School, USA

University of Cádiz/INiBICA, Spain

CNRS – IINS, University of Bordeaux, France

Keynote Speakers

Eileen Furlong – University of Heidelberg, Germany
Kenneth Harris – UCL Queen Square Institute of Neurology, UK
Ed Lein – Allen Institute for Brain Science, USA
John Marioni – European Bioinformatics Institute (EMBL-EBI), UK
Ana Martin-Villalba – University of Heidelberg, Germany
Samantha Morris – Washington University, St Louis, USA
Rahul Satija – New York Genome Center (NYGC), USA
Kun Zhang – Department of Bioengineering, University of California, USA

Instructors

Marek Bartosovic – Karolinska Institutet, Sweden
Lisa Bast – Karolinska Institutet, Sweden
Song Chen – San Diego, USA
Hattie Chung – Broad Institute/MIT, USA
Lisbeth Harder – Karolinska Institutet, Sweden
Martin Häring – University Clinic Münster, Germany
Hannah-Sophie Hochgerner – Technion – Israel Institute of Technology
Danny Kitseberg – ELSC, Jerusalem University, Israel
Gioele La Manno – EPFL, Lausanne
Christoffer Mattsson Langseth – Stockholm University, Sweden
Christian Mayer – Max Planck Institute, Germany
Viktor Petukhov – University of Copenhagen, Denmark
Milda Valiukonyte – Karolinska Institutet, Sweden

Course content

Topics & Techniques

During this course, students will get hands-on experience with entire single-cell transcriptomic projects from tissue dissociation to publishable figures. We will teach the use of different kinds of starting material, three different sequencing techniques, how to treat the raw sequencing data and a multitude of analytical tools. After attending the course, our goal is that the students should be able to go back to their institute and have enough knowledge and understanding to initiate well-designed single-cell sequencing projects to tackle important questions in Neuroscience.

The course will cover following topics:

  • Cell classification in the nervous system and its implication on how we do neuroscience
  • Discrete versus continuous variability in gene expression
  • Single-cell transcriptomics and analysis of disease
  • advantages and disadvantages of different techniques; RNA amplification, SmrtSeq, SplitSeq, Dropseq, 10X genomics,
  • What type of biological insights can be gained from single cell transcriptomics
  • multimodal analysis of single cell biology where transcriptomics is coupled with other biological parameters such as a cell’s morphology, tissue localization, epigenome, proteome and/or function
  • Preparation and isolation of single cell, nuclei isolation, RNA isolation, single cell RNA amplification procedures, library construction for sequence analysis and RNA sequencing.
  • experimental design considerations, data processing, data handling, quality control of the sequencing data, understanding the variances of the data, clustering of cell types
  • Nervous system development and other dynamical processes including lineage tracing including RNA-Velocity and pseudotime analysis

Projects

For more information on projects download the “Projects list”.

– Project 1: Visualization and quantification of cellular complexity of the CA1 region of the
mouse brain

– Project 2: Understanding cellular maturation during the development of the embryonic
nervous system by whole-cell RNA seq

– Project 3: GABAergic neuronal diversity across different forebrain structures

– Project 4: Single whole cells analysis of an Alzheimer’s disease mouse model

– Project 5: Single nuclei analysis of an Alzheimer’s disease mouse model

– Project 6: Single nuclei analysis of GABAergic cells in the dorsal horn in a chronic pain
model

– Project 7: Single whole cells analysis of GABAergic cells in the dorsal horn in a chronic pain model

– Project 8: Large scale single-cell RNA-sequencing of brain tissue using SPLiT-Seq

Project 9: Single-cell profiling of histone modifications in the mouse cortex using scCUT&Tag

– Project 10: InCiteSeq

– Computational Projects: state-of-the-art approaches for computational analysis and interpretation of single-cell RNA-seq data.

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 : 3.500 € (includes tuition fee, accommodation and meals)

Applications closed on 21st February 2022

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.

Course sponsors

Interacting with neural circuits

Course overview

Understanding the links between activity in neural circuits and behavior is a fundamental problem in neuroscience. Attacking this problem requires detailed information about the cell types in neural circuits and their connectivity, and recording the spatiotemporal patterns of activity in the intact brain during behaviour. Furthermore, probing causal relationships between cellular and circuit-level processes and behaviour requires perturbation of specific elements of the circuit in a temporally and spatially precise manner.

This course will highlight the new anatomical, genetic, optical, electrophysiological, optogenetic, and pharmacogenetic approaches that are available for addressing these challenges. The faculty will discuss tool development through to their implementation in diverse model systems, including mice and zebrafish. Students will learn the potential and limitations of these techniques, allowing them to both design and interpret experiments correctly.

Course directors

Michael Hausser

Course Director

Wolfson Institute for Biomedical Research, UCL, UK

Claire Wyart

Course Director

Paris Brain Institute, ICM, France

Tiago Branco

Course Director

Sainsbury Wellcome Centre, UK

Susana Lima

Course Director

Champalimaud Foundation, Portugal

Keynote Speakers

Isaac Bianco, University College London, UK
Ed Boyden, Massachusetts Institute of Technology, USA
Michael Brecht, Bernstein Center for Computational Neuroscience, Germany
Megan Carey, Champalimaud Foundation, Portugal
Eugenia Chiappe, Champalimaud Foundation, Portugal
Winfried Denk, Max Planck Institute of Neurobiology, Germany
Emily Dennis, HHMI, Janelia, USA
Valentina Emiliani, Vision Institute, France
Ken Harris, University College London, UK
Greg Jefferis MRC Laboratory of Molecular Biology, UK
Na Ji, University of California, USA
Mackenzie Mathis, EPFL, Switzerland
Marta Moita, Champalimaud Foundation, Portugal
Francois St-Pierre, Baylor College of Medicine, USA

Michael Orger, Champalimaud Foundation, Portugal
Marius Pachitariu, HHMI, Janelia, USA
Darcy Peterka, Columbia University, USA
Pavan Ramdya, EPFL, Switzerland
Ana João Rodrigues, ICVS, Minho University, Portugal
Botond Roska, Institute of Molecular and Clinical Ophthalmology, Switzerland
Nick Steinmetz, University of Washington, USA
Carsen Stringer, HHMI, Janelia, USA
Karel Svoboda, HHMI, Janelia, USA
Scott Waddell, Oxford University, UK
Chris Xu, Cornell University, USA
Ofer Yizhar, Weizmann Institute of Science, Israel

Instructors

Dustin Herrmann, Wolfson Institute for Biomedical Research, UCL, UK
Maxime Beau, Wolfson Institute for Biomedical Research, UCL, UK
Edgar Baumler, Wolfson Institute for Biomedical Research, UCL, UK
Moritz Buchholz, Wolfson Institute for Biomedical Research, UCL, UK
Maha Dhanasekar, Paris Brain Institute, ICM, France
Pierre Tissier, Paris Brain Institute, ICM, France
Martin Carbó-Tano, Paris Brain Institute, ICM, France
Olivier Mirat, Paris Brain Institute, ICM, France
Dario Campagner,
Sainsbury Wellcome Centre, UK
Tan YuLin,
Sainsbury Wellcome Centre, UK
Hugo Marques,
Champalimaud Foundation, Portugal
Ana Gonçalves,
Champalimaud Foundation, Portugal

Course content

Topics & Techniques

The course combines a lecture series featuring top speakers from around the world with a practical “hands-on” introduction to the latest methods for probing neural circuits, using drosophila, zebrafish, and (transgenic) mice. The course will focus on anatomy and connectivity, recording and manipulation, and the relation between circuits and behavior. During the course, each student will carry out a ‘mini-project’, executed under the guidance and supervision of experienced researchers and teaching assistants. Techniques used during the course include:

Zebrafish

  • optogenetic manipulation using digital holography;
  • behavior & population calcium imaging using 2-photon microscopy;

Mice

  • In vivo 2-photon and 3-photon imaging;
  • all-optical interrogation (simultaneous 2-photon optogenetics and 2-photon imaging);
  • miniscope imaging;
  • extracellular recordings of neural population activity using Neuropixels probes in head-fixed and freely behaving animals;
  • intracellular electrophysiological recordings using whole-cell patch-clamp;
  • viral tracing, histology preparation, expansion microscopy, and fluorescence imaging techniques.

For more information on the course programme, you can visit the past course website.

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 : 3.500 € (includes tuition fee, accommodation and meals)

Application closed on 24th January 2022

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

At Scientifica, we employ experience, collaboration, and superior design to empower you to discover the brain’s secrets and overcome neurological diseases. Our equipment is optimised for electrophysiology, multiphoton imaging and optogenetics studies.

Our highly qualified team provides first-class service and support, and our resources centre is packed with invaluable and educational content. Get in touch to see how we can help you achieve your research goals.

Computational Neuroscience

Course overview

Computational Neuroscience is a rapidly evolving field whose methods and techniques are critical for understanding and modelling the brain, and also for designing and interpreting experiments. Mathematical modelling is an essential tool to cut through the vast complexity of neurobiological systems and their many interacting elements.

The course teaches the central ideas, methods, and practices of modern computational neuroscience through a combination of lectures and hands-on project work. During the course’s mornings, distinguished international faculty deliver lectures on topics across the entire breadth of experimental and computational neuroscience. For the remainder of the time, students work on research projects in teams of 2 to 3 people under close supervision of expert tutors and faculty. Research projects are proposed by faculty before the course, and include the modeling of neurons, neural systems, and behavior, the analysis of state-of-the-art neural data (behavioral data, multi-electrode recordings, calcium imaging data, connectomics data, etc.), and the development of theories to explain experimental observations.

Course directors

Brent Doiron

Course Director

University of Chicago, US

Geffen

Maria Geffen

Course Director

University of Pennsylvania, US

Gjorgjieva

Julijana Gjorgjieva

Course Director

Max Planck Institute for Brain

Research, Germany

Joe Paton

Course Director

Champalimaud Foundation, Portugal

Keynote Speakers

Alex Cayco-Gajic – École Normale Supérieure, France
John Krakauer – Johns Hopkins University, USA
Maté Lengyel – Cambridge University, UK
Ashok Litwin-Kumar – Columbia University, USA
Christian Machens – Champalimaud Foundation, Portugal
Olivier Marre – Vision Institute, France
Ken Miller – Columbia University, USA
Srdjan Ostojic – École Normale Supérieure, France
Anne-Marie Oswald – University of Pittsburgh, USA
Saskia de Vries, Allen Institute, USA
Alfonso Renart – Champalimaud Foundation, Portugal
Megan Carey – Champalimaud Foundation, Portugal
Gilles Laurent – Max Planck Institute for Brain Research, Germany

Instructors

Dylan Festa – Max Planck Institute for Brain Research, Germany

Course content

Projects

Project 1. Emergence of selectivity through the interplay of Hebbian and homeostatic plasticity in neuronal networks (Gjorgjieva)

Project 2. Neural circuits for the generation of locomotor behavior (Gjorgjieva)

Project 3. Analysis of multi-neuron spike time series data from the locust olfactory system (Laurent)

Project 4. Reinforcement learning as a model for decision making (Paton & Lloyd)

Project 5. Finding structure in natural behavior (Murthy)

Project 6. The SSN: Dynamic behavior, effects of adaptive and saturating mechanisms and of network noise (Miller & Doiron)

Project 7. Uncovering synaptic plasticity rules from experiments (Stein)

Project 8. Implementing linear, nonlinear, and chaotic computations in spike coding networks (Keemink)

Project 9.Teaching animals to respond without bias by teaching algorithms to find bias (Macke)

Project 10.Predicting responses of single neuron in vitro: Mechanistic vs LIF models (Gonçalves & Macke)

Project 11. The role of inhibitory neurons in sound adaptation (Geffen)

Project 12. The neuronal circuit for hearing under uncertainty (Geffen)

Preliminary programme

All days are structured with lectures in the morning and experimental learning & tutorials – followed by discussion – in the afternoon

Week 1

17-22 July

  • Arrival and Welcome reception

  • Introduction and Single-Neuron Dynamics

  • Statistical analysis of neural data

  • Network dynamics

  • Normative models

  • Physical Constraints on Computing

23-24 July

Social event and free time

Week 2

25-29 July

  • Sensory coding and receptive fields

  • Spatial coding and memory

  • Vision

  • Neural Circuits and Synaptic Plasticity

  • Map formation and self-organization

30-31 July

Social event and free time

Week 3

1-5 August

  • Balanced Networks & Efficient Population Coding

  • Dendritic Computations & Birdsong Production

  • Reinforcement learning

  • Project work and presentations

6 August

Departure

For more information on the course programme, you can visit the past course website.

Pre-school in Mathematics and Programming (12-15 July)

The Computational Neuroscience course targets both students with a biological/experimental background (“experimentalists”) and ones with a quantitative background (“theorists”). Two primary objectives of the course are to help students cross the traditional discipline boundaries that most are still trained in, and to get experimentalists and theorists to collaborate on a research project.

For the experimentalists, this often means catching up on their math and programming skills; for the theorists, on their (neuro-)biology. Because course projects will be computer-based, “catching up” is asymmetrical. When theorists engage on a course project, they can usually get by with limited neurobiological background. When experimentalists engage on a course project, however, they need some proficiency in programming and a solid understanding of the underlying mathematics.

To level the playing field and counterbalance this asymmetry, we offer an optional pre-school that teaches students with little or no programming skills the basics of modern programming languages (e.g., MATLAB or Python). The pre-school will also provide refreshers on standard math topics such as linear algebra and calculus, important to better follow the course. While a four-day school cannot be a replacement for the mathematical education that students from quantitative disciplines enjoy, it will give students a sufficient head-start to focus on lecture contents and the research projects, once the main course starts.

Unsure on whether to attend the preschool? It’s easy: if you have no knowledge of MATLAB or Python, then you should take the preschool. If you do know how to program in these languages, then it depends on your math background. Check out our little exam here to test your skills. Try to answer as many questions as possible within twenty minutes. The solutions are here.

Self-evaluation:

  • If you managed to do all exercises (and you have some knowledge of MATLAB/Python) then you should skip the pre-school.
  • If you more or less managed everything, with a few difficulties here or there (but you do know how to work in MATLAB/Python) then the pre-school may be a good idea, but you should consider it optional.
  • If you managed to solve exercises 1 to 6, but had difficulties afterwards, then you should take the pre-school.
  • If you had many problems in exercises 1 to 6, and the rest was pretty incomprehensible, then we’d strongly recommend to catch up on your high school math first before taking either the pre-school or the main course. Experience has shown that you will get very little out of the course without a solid background in quantitative thinking

Please note, that there is an additional fee for the pre-school: 500 EUR , which covers tuition, housing, and boarding for the extra days. Applications to the pre-school are part of the application to the main course.

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 : 2.500 € (includes tuition fee, accommodation and meals)

Pre-school fee: 500 €

Applications closed on 28th March 2022

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.

Advanced approaches to neuro evo-devo

Course overview

This course is a theoretical and practical training course on neurodevelopment and its evolution. It will provide an overview of the current concepts and knowledge on central nervous system development in several species, including invertebrates, mice, and humans, and their link to diseases. It will combine lectures and hands-on projects on convergent and divergent developmental processes across species at the molecular, cellular, circuit, and behavioural levels, including those relevant for human disease. It will include methods in genetics and molecular biology (e.g. genome editing), cellular neuroscience (e.g. transplantations), circuit neuroscience (e.g. live imaging) and -omics (e.g scRNA seq and bioinformatics).

This course will provide participants with a broad yet practical understanding of how the brain develops in different species, and how modern genetic approaches now allow cross-species comparisons to identify key developmental mechanisms. It is intended for PhD students and early-career postdocs.

Course directors

Denis Jabaudon

Denis Jabaudon

Course director

Faculty of Medicine,
University of Geneva, Switzerland

Paris Brain Institute, Institut du Cerveau (ICM), France

Claude Desplan

Claude Desplan

Co-director

Department of Biology, NYU New York, USA

Emilie Pacary

Emilie Pacary

Co-director

Neurocentre Magendie, University of Bordeaux, France

Keynote Speakers

Laure Bally-Cuif – Institut Pasteur, France
Sonia Garel – Ecole Normale Superieure (ENS), France
Simon Hippenmeyer – Institute of Science and Technology (IST), Austria
Oliver Hobert – Columbia University , USA
Guillermina Lopez Bendito – Instituto de Neurociencias – UMH-CSIC, Spain
Shubha Tole – Tata Institute of Fundamental Research, India

Instructors

Alexandre Baffet – Institut Curie, France
Nathan Benac – University of Bordeaux, France
Sara Bizzotto – Paris Brain Institute, France
Boyan Bonev – Helmholtz Zentrum München, Germany
Antoine de Chevigny – INMED, Univeristy of Marseille, France
Fernando García-Moreno, Achucarro Basque Center for Neuroscience, Bilbao, Spain
Juliette Godin – IGBMC Univeristy of Strasbourg, France
Isabel Holguera – New York University, USA
Nathalie Jurisch – Kavli Institute for Systems Neuroscience – NTNU, Norway
Karine Loulier – Institute for Neurosciences of Montpellier, France
Esther Klingler – UNIGE, Switzerland
Nikos Konstantinides – Institut Jacques Monod, France
Pierre Mortessagne – Neurocentre Magendie, Univeristy of Bordeaux, France
Homaira Nawabi – Grenoble Institute of Neuroscience, France
Stéphane Nédélec – Institut du Fer à Moulin, France
Sergi Roigg Puigros – UNIGE, Switzerland
Julie Stoufflet – Giga Liège, Belgium
Emre Yaksi – Kavli Institute for Systems Neuroscience – NTNU, Norway

Course content

Techniques

  • Crispr-CAS9 mediated genome editing to tag endogenous actin
  • Dissection and dissociation of mouse cortex
  • Fly husbandry
  • Human induced pluripotent stem cells culture
  • In utero/ex-utero electroporation
  • Analyses of cell position and protein expression using ImageJ
  • analyses of migration
  • ATAC-seq library preparation
  • Cell culture (dissociated hippocampal neurons, COS-7), cell transfection
  • Comparative neuroanatomy
  • Confocal microscopy and image analysis
  • Culture of organotypic brain slices
  • Drosophila brain dissection at L3 stage
  • Functional brain imaging in adult, juvenile and larval zebrafish and associated data analysis
  • Genetic manipulation of tTFs in neuroblasts using MARCM
  • Immunofluorescence
  • Image reconstructions and 3D analysis
  • Immunohistochemistry
  • Immunostaining
  • Intravitreal & in utero injections
  • Introduction to bioinformatics and scRNAseq analysis
  • Live birth-dating of neurons and functional imaging of their activity
  • Microtome / Vibratome sectioning
  • Retina, optic nerve dissection & explant culture
  • Spheroid generation and differentiation
  • Tissue freezing and cryostat slicing
  • Videomicroscopy,time lapse recording

See more techniques in the projects list.

Projects

  • Project 1 : “Live imaging of microtubule dynamics in mouse brain slices”
  • Project 2 : “Role of dopamine-glutamate interplay during synaptogenesis”
  • Project 3 : “Studying a developmental mosaic brain disorder in human cortical spheroids”
  • Project 4: “Histological and transcriptional analysis of isochronically labelled cortical neurons”.
  • Project 5: “Studying the morphological properties of developmentally- and adult-born dentate granule neurons”
  • Project 6: “RGC manipulation to modulate CNS regeneration”
  • Project 7: “Study of neuronal migration after prenatal alcohol exposure”
  • Project 8 : “Genome-wide profiling of the epigenome and the transcriptome of major cell types from the developing mouse cortex”
  • Project 9: “Emergence of intracortically-projecting neuron diversity”
  • Project 10 : “Studying the effect of temporal series in the proliferative capacity of Drosophila neural stem cells”
  • Project 11: “MAGIC Markers strategies to investigate neuron-astrocyte anatomical relationships during cortical development”
  • Project 12: “ Differentiation of spinal organoids and motor neuron subtypes from human induced pluripotent stem cells”
  • Project 13: “Inferring ligand-receptor interactions between GABAergic and Glutamatergic cells during Somatosensory Cortex Development”
  • Project 14: “Imaging actin cytoskeleton dynamics during radial migration of projection neurons in the mouse developing cortex”.
  • Project 15: “Neurogenesis in the Drosophila optic lobe by temporal patterning”
  • Project 16: “Fluid dynamics in the brain of zebrafish and medaka larvae”
  • Project 17: “Imaging function, connectivity, and development of brain circuits in zebrafish”
  • Project 18: “Comparative neurodevelopment of mouse and chick brains”

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 : 3.500 € (includes tuition fee, accommodation and meals)

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.