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


Neurocentre Magendie, INSERM U1215, University of Bordeaux, France

Cyril Herry


Neurocentre Magendie, INSERM U1215, University of Bordeaux France

Keynote speakers

Antoine Adamantidis – University of Bern, Switzerland

Athena Akrami – University College London, UK

Benjamin Grewe – ETH Zurich, Switzerland

Matteo Carandini – University College London, UK

Megan Carey – Champalimaud Centre, Portugal

Marie Carlen – Karolinska Institute, Sweden

Valentina Emiliani – Vision Institute Paris, France

Rainer Friedrich – FMIBR, Switzerland

Nadine Gogolla – Max Planck Institute of Neurobiology, Germany

Johannes Kohl – Francis Crick Institute, UK

Matthew E. Larkum – Humboldt University of Berlin, Germany

Tommaso Patriarchi – University of Zurich, Switzerland

Pavan Ramdya – EPFL, Switzerland

Nathalie Rochefort – University of Edinburgh, UK

Lisa Roux – Bordeaux Neurocampus, France

Manuel Zimmer – University of Vienna, Austria

Please note this list is subject to change


Arthur Leblois – Bordeaux Neurocampus, France

Catherine Marneffe – Bordeaux Neurocampus, France

Christopher Lewis – Univeristy of Zurich – Switzerland

Cyril Herry – Bordeaux Neurocampus, France

Gabrielle Girardeau – Institut du Fer à Moulin, France

Gwendolin Schoenfeld – Univeristy of Zurich – Switzerland

Jean-Sebastien Jouhanneau – MDC Berlin (Germany

Jerôme Baufretton – Bordeaux Neurocampus, France

Lisa Roux – Bordeaux Neurocampus, France

Lorena Delgado – Bordeaux Neurocampus, France

Marie Labouesse – ETH Zurich – Switzerland

Naoya Takahashi – Bordeaux Neurocampus, France

Nikita Vladimirov – Univeristy of Zurich – Switzerland

Ourania Semelidou – Bordeaux Neurocampus, France

Pavan Ramdya   EPFL Lausanne – Switzerland

Philipp Bethge   Univeristy of Zurich – Switzerland

Roman Boehringer – ETH Zurich – Switzerland

Roman Ursu – Bordeaux Neurocampus, France

Sandra Soukup – Bordeaux Neurocampus, France

Tom Broyer – Bordeaux Neurocampus, France

Yann Humeau – Bordeaux Neurocampus, France

Yuktiben Vyas – Bordeaux Neurocampus, France

Course content

                               Topics & Techniques

During the course students will learn all basics 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; 

– basics 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; 


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 lightsheet 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’’


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.

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